--- doc/loncapafiles/loncapafiles.lpml	2002/03/02 22:33:16	1.106
+++ doc/loncapafiles/loncapafiles.lpml	2003/12/05 23:12:31	1.302
@@ -1,7 +1,8 @@
+<!DOCTYPE lpml PUBLIC "-//TUX/DTD lpml 1.0 Final//EN"
+ "http://lpml.sourceforge.net/DTD/lpml.dtd">
 <!-- loncapafiles.lpml -->
-<!-- Scott Harrison -->
 
-<!-- $Id: loncapafiles.lpml,v 1.106 2002/03/02 22:33:16 harris41 Exp $ -->
+<!-- $Id: loncapafiles.lpml,v 1.302 2003/12/05 23:12:31 www Exp $ -->
 
 <!--
 
@@ -46,7 +47,7 @@ http://www.lon-capa.org/
 !!! 127.0.0.1  localhost.localdomain  localhost !!!
 !!! 35.2.3.80  computer1 computer1.notreal.msu.edu !!!
 </specialnotice>
-<specialnotice dist='redhat7.0 redhat7.1'>
+<specialnotice dist='redhat7 redhat7.1'>
 !!!!!!!!!  REDHAT 7.*   NOTICE   !!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!  LINE IN Cookie.pm     !!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!  MUST BE REPLACED DUE  !!!!!!!!!!!!!!!!!!!!
@@ -98,6 +99,14 @@ http://www.lon-capa.org/
   <chmod dist='default'>0444</chmod><chown dist='default'>root:root</chown>
   <abbreviation>static</abbreviation>
 </category>
+<category name="www static conf" type="runtime">
+  <chmod dist='default'>0644</chmod><chown dist='default'>www:www</chown>
+  <abbreviation>static</abbreviation>
+</category>
+<category name="www static conf" type="development">
+  <chmod dist='default'>0644</chmod><chown dist='default'>www:www</chown>
+  <abbreviation>static</abbreviation>
+</category>
 <category name="conf" type="runtime">
   <chmod dist='default'>0644</chmod><chown dist='default'>root:root</chown>
   <abbreviation>configurable</abbreviation>
@@ -138,6 +147,14 @@ http://www.lon-capa.org/
   <chmod dist='default'>0644</chmod><chown dist='default'>root:root</chown>
   <abbreviation>systemfile</abbreviation>
 </category>
+<category name="system script" type="runtime">
+  <chmod dist='default'>0755</chmod><chown dist='default'>root:root</chown>
+  <abbreviation>systemscript</abbreviation>
+</category>
+<category name="system script" type="development">
+  <chmod dist='default'>0755</chmod><chown dist='default'>root:root</chown>
+  <abbreviation>systemscript</abbreviation>
+</category>
 <category name="root script" type="runtime">
   <chmod dist='default'>0700</chmod><chown dist='default'>root:root</chown>
   <abbreviation>rootscript</abbreviation>
@@ -214,112 +231,119 @@ echo '**********************************
 <rpmRequires>
 <item>PreReq: LON-CAPA-setup</item>
 <item>PreReq: apache</item>
-<item>PreReq: /etc/httpd/conf/access.conf</item>
+<item>PreReq: /etc/httpd/conf/httpd.conf</item>
 </rpmRequires>
 </rpm>
 <directories>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for configuration files</description>
 </directory>
-<directory>
-  <targetdir dist='default'>etc/atalk</targetdir>
-  <categoryname>standard</categoryname>
-  <description>appletalk configuration files</description>
-</directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/cron.d</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for running time-based "jobs"
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/httpd/conf</targetdir>
   <categoryname>standard</categoryname>
   <description>web configuration files</description>
 </directory>
-<directory>
-  <targetdir dist='default'>etc/ntp</targetdir>
-  <categoryname>standard</categoryname>
-  <description>configuration directory for network time protocol</description>
-</directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/pam.d</targetdir>
   <categoryname>standard</categoryname>
   <description>configuration directory for password authentication mechanism
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/init.d</targetdir>
-  <targetdir dist='debian2.2'>etc/init.d</targetdir>
+  <targetdir dist='debian'>etc/init.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run during system startup</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc0.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc0.d</targetdir>
+  <targetdir dist='debian'>etc/rc0.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 0</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc1.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc1.d</targetdir>
+  <targetdir dist='debian'>etc/rc1.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 1</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc2.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc2.d</targetdir>
+  <targetdir dist='debian'>etc/rc2.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 2</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc3.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc3.d</targetdir>
+  <targetdir dist='debian'>etc/rc3.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 3</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc4.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc4.d</targetdir>
+  <targetdir dist='debian'>etc/rc4.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 4</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc5.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc5.d</targetdir>
+  <targetdir dist='debian'>etc/rc5.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 5</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc6.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc6.d</targetdir>
+  <targetdir dist='debian'>etc/rc6.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 6</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lonTabs</targetdir>
   <categoryname>standard</categoryname>
   <description>tab-formatted reference files</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd</targetdir>
   <categoryname>standard</categoryname>
   <description>start of the web server tree</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/perl</targetdir>
   <categoryname>server readonly</categoryname>
   <description>perl scripts for managing the LON-CAPA system</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/perl/logs</targetdir>
   <categoryname>server standard</categoryname>
   <description>location where system performance and error logs are kept
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/lon-status/londchld</targetdir>
   <categoryname>server standard</categoryname>
   <description>
@@ -327,114 +351,211 @@ Used by lond parent to check if children
 (otherwise they are killed and replaced).
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/perl/tmp</targetdir>
   <categoryname>server standard</categoryname>
   <description>location where temporary files (for caching) are stored
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/prtspool</targetdir>
   <categoryname>server standard</categoryname>
   <description>for the output of lonprintout.pm
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/lib</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>location of LON-CAPA software modules and
+extensions</description>
+</directory>
+<directory dist='default'>
+  <!-- Must protect localauth.pm from extinction. -->
+  <protectionlevel>weak_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lib/perl</targetdir>
   <categoryname>server readonly</categoryname>
   <description>location of LON-CAPA non web mod-perl handlers</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lib/perl/Apache</targetdir>
   <categoryname>server readonly</categoryname>
   <description>location of LON-CAPA web mod-perl handlers</description>
 </directory>
-<directory>
-  <targetdir dist='default'>home/httpd/lonIDs</targetdir>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/lib/perl/Apache/localize</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>location of LON-CAPA MakeText translation files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/lib/perl/HTML</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>location of HTML specific perl module fixes and additions
+  </description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/lib/perl/LONCAPA</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>location of HTML specific perl module fixes and additions
+  </description>
+</directory>
+<directory dist='default'>
+   <protectionlevel>modest_delete</protectionlevel>
+ <targetdir dist='default'>home/httpd/lonIDs</targetdir>
   <categoryname>server standard</categoryname>
   <description>cookie jar</description>
 </directory>
-<directory>
+<directory dist='default'>
+   <protectionlevel>modest_delete</protectionlevel>
+ <targetdir dist='default'>home/httpd/scantron</targetdir>
+  <categoryname>server standard</categoryname>
+  <description>uploaded scantron forms directory</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/sockets</targetdir>
   <categoryname>server standard</categoryname>
   <description>lonc's sockets</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/sockets/delayed</targetdir>
   <categoryname>server standard</categoryname>
   <description>lonc's sockets (delayed)</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/cgi-bin</targetdir>
   <categoryname>standard</categoryname>
   <description>location of cgi scripts</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html</targetdir>
   <categoryname>server standard</categoryname>
   <description>location of web-accessible file tree</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res</targetdir>
   <categoryname>server standard</categoryname>
   <description>root of resource tree</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/userfiles</targetdir>
+  <categoryname>server standard</categoryname>
+  <description>root for user uploaded files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm</targetdir>
   <categoryname>server readonly</categoryname>
   <description>unauthenticated resources</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/rat</targetdir>
   <categoryname>server readonly</categoryname>
   <description>home of the rat</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/help</targetdir>
   <categoryname>server readonly</categoryname>
   <description>online help documentation</description>
 </directory>
-<directory>
-  <targetdir dist='default'>home/httpd/html/adm/help/api</targetdir>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/jme</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>JME support files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/helper</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>XML specifications for helpers</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/gif</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation gif files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/eps</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation eps files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/tex</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation tex files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/png</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation png files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/lib/perl</targetdir>
   <categoryname>server readonly</categoryname>
   <description>online help documentation for the LON-CAPA programming
 interface</description>
 </directory>
-<directory>
-  <targetdir dist='default'>home/httpd/html/adm/help/api/Apache</targetdir>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/lib/perl/Apache
+  </targetdir>
   <categoryname>server readonly</categoryname>
   <description>online help documentation for the LON-CAPA programming
 interface, Apache (mod_perl) handlers</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/help/scripts</targetdir>
   <categoryname>server readonly</categoryname>
   <description>online help documentation for the LON-CAPA programming
 interface, Apache (mod_perl) handlers</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/lonIcons</targetdir>
   <categoryname>server readonly</categoryname>
   <description>graphic widgets</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/lonMisc</targetdir>
   <categoryname>server readonly</categoryname>
   <description>miscellaneous resources</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/lonKaputt</targetdir>
   <categoryname>server readonly</categoryname>
   <description>error warnings and icons</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lonUsers</targetdir>
   <categoryname>server standard</categoryname>
   <description>Home directories of local users.  There is a five-tier
 structure to the directories:
 [domain]/[firstletter]/[secondletter]/[thirdletter]/[userid].  For example,
 a user fredflint at MSU would have his information located in
-lonUsers/msu/f/r/e/fredflint.<br />&nbsp;<br />Within this directory there are
+lonUsers/msu/f/r/e/fredflint.<br />&#160;<br />Within this directory there are
 a variety of files which govern the scope of what a user can do within the
 LON-CAPA system.  A passwd file determines the type of authentication
 mechanism to use.
@@ -442,80 +563,152 @@ mechanism to use.
 roles.db) which specify the roles and privileges for a user in the
 LON-CAPA system.</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/MathML</targetdir>
   <categoryname>server readonly</categoryname>
   <description>mathematics markup language resources</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/res/lib/templates</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Resource library
+  </description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/includes</targetdir>
   <categoryname>server readonly</categoryname>
   <description>files useful for including within customized scripting
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/includes/templates
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description>template files useful for customized scripts</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/lon-status</targetdir>
   <categoryname>server standard</categoryname>
-  <description>status reports</description>
+  <description>status reports; online logs are kept that
+are viewable over the world-wide web</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages</targetdir>
   <categoryname>server readonly</categoryname>
   <description>web user interface resources</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/res/adm/pages/reactionresponse</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>web user interface resources</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/lonLCDfont</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>LCD font for remote control</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/lonDomLogos</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Logos for LON-CAPA domains</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/lonTabs/lonDomColors</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Designs for LON-CAPA domains</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/lonInterFace</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Page headers and graphical interface files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages/bookmarkmenu
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description>bookmark user interface code</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages/annotations
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description></description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages/indexericons
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description>icons that help depict the file system (outdated)</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/lib/perl5/site_perl/5.005</targetdir>
-  <targetdir dist='redhat7.1'>usr/lib/perl5/site_perl/5.6.0</targetdir>
-  <targetdir dist='debian2.2'>usr/local/lib/perl/5.6.0</targetdir>
+  <targetdir dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0</targetdir>
+  <targetdir dist='redhat8 redhat9'>usr/lib/perl5/site_perl/5.8.0</targetdir>
+  <targetdir dist='debian'>usr/local/lib/perl/5.6.0</targetdir>
   <categoryname>standard</categoryname>
   <description>system perl tree (usually present on linux systems)
   </description>
 </directory>
-<directory>
-  <targetdir dist='default'>usr/local/bin</targetdir>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/bin</targetdir>
+  <categoryname>standard</categoryname>
+  <description>local binary files for loncapa</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/doc</targetdir>
   <categoryname>standard</categoryname>
-  <description>local binary files</description>
+  <description>local documentation files for loncapa</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/doc/conf_examples</targetdir>
+  <categoryname>standard</categoryname>
+  <description>examples of configuration files for secondary
+ services</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/sbin</targetdir>
+  <categoryname>standard</categoryname>
+  <description>local "auxiliary" binary files for loncapa</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/local/man/man1</targetdir>
   <categoryname>standard</categoryname>
   <description>local manual pages</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/man/man1</targetdir>
   <categoryname>standard</categoryname>
   <description>manual pages</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/man/man3</targetdir>
   <categoryname>standard</categoryname>
   <description>manual pages</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/sbin</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for superuser executables</description>
@@ -524,8 +717,8 @@ LON-CAPA system.</description>
 <files>
 <file>
 <source>loncom/krb.conf</source>
-<target dist='default'>etc/krb.conf</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/krb.conf</target>
+<categoryname>static conf</categoryname>
 <description>
 which Kerberos server to contact for specified Kerberos domains
 </description>
@@ -550,25 +743,23 @@ each list element consists of only two s
 <target dist='default'>etc/httpd/conf/loncapa.conf</target>
 <categoryname>conf</categoryname>
 <description>
+<p>
 The goal of this file is to implement all LON-CAPA specific
-customization of the Apache web server.
-</description>
-</file>
-<file>
-<source>loncom/access.conf</source>
-<target dist='default'>etc/httpd/conf/access.conf</target>
-<categoryname>conf</categoryname>
-<description>
-This file has two major functions.
-For the Apache web server, it defines a global
-access configuration which defines what server options (Indexes", "Includes",
-"FollowSymLinks", "ExecCGI", or "MultiViews") are associated
-with specific directories ("/", "/home/httpd/html", "/home/httpd/cgi-bin",
-and "/usr/doc").  For the LON-CAPA network server and perl module
-handlers, it defines machine specific settings (lonHostID, lonRole,
-lonAdmEMail, lonDefDomain, lonLoadLim, lonExpire, and lonReceipt)
-and internal machine settings for specific directories, socket ports,
-and browser detection logic.
+customization of the Apache web server (most all of these values
+require manual input from the system administrator at some point).
+The values in this file, as opposed to loncapa_apache.conf, are
+meant to be machine and institution specific.
+</p>
+<p>
+For the LON-CAPA network server and perl module
+handlers, it defines machine specific settings including lonHostID, lonRole,
+lonAdmEMail, lonDefDomain, lonLoadLim, lonExpire, and lonReceipt.
+</p>
+<p>
+This file should not be viewable by regular users of the system.
+Only root and www should be able to view the contents of this file
+since lonReceipt is sensitive.
+</p>
 </description>
 <note>
 <b>configure</b>
@@ -590,6 +781,25 @@ MySQL database</td></tr>
 </note>
 </file>
 <file>
+<source>loncom/loncapa_apache.conf</source>
+<target dist='default'>etc/httpd/conf/loncapa_apache.conf</target>
+<categoryname>static conf</categoryname>
+<description>
+The goal of this file is to implement all LON-CAPA specific
+customization of the Apache web server that does not require
+user input.
+
+For the Apache web server, it defines a global
+access configuration which defines what server options (Indexes", "Includes",
+"FollowSymLinks", "ExecCGI", or "MultiViews") are associated
+with specific directories ("/", "/home/httpd/html", "/home/httpd/cgi-bin",
+and "/usr/doc").  For the LON-CAPA network server and perl module
+handlers, it defines 
+and internal machine settings for specific directories, socket ports,
+the www@localhost MySQL password, and browser detection logic.
+</description>
+</file>
+<file>
 <source>loncom/startup.pl</source>
 <target dist='default'>etc/httpd/conf/startup.pl</target>
 <categoryname>static conf</categoryname>
@@ -597,17 +807,22 @@ MySQL database</td></tr>
 This file provides initializations for perl handlers.  It adjusts what
 the module path space is (so as to include /home/httpd/lib/perl/Apache) as
 well as causing the Apache module to be used for every perl handler.
-<tt>startup.pl</tt> is invoked by <tt>access.conf</tt>.
+<tt>startup.pl</tt> is invoked by <tt>loncapa_apache.conf</tt>.
 </description>
 </file>
 <file>
-<source>loncom/publisher/thesaurus.dat</source>
-<target dist='default'>home/httpd/lonTabs/thesaurus.dat</target>
-<categoryname>static conf</categoryname>
+<source>loncom/thesaurus/thesaurus.db</source>
+<target dist='default'>home/httpd/lonTabs/thesaurus.db</target>
+<categoryname>system file</categoryname>
 <description>
-Custom Thesaurus file for LON-CAPA, in the format
-word@wordID@frequency@relatedwordID:frequency,relatedwordID:frequency,...
+Thesaurus database file to be built from loncom/thesaurus/rawkey.txt
 </description>
+<build trigger='always run'>
+loncom/thesaurus/build_thesaurus_wrapper.sh
+</build>
+<dependencies>
+rawkey.txt
+</dependencies>
 </file>
 <file>
 <source>loncom/interface/mydesk.tab</source>
@@ -626,8 +841,16 @@ Descriptive list of file extensions, and
 </description>
 </file>
 <file>
-<source>loncom/cgi/barcode.gif</source>
-<target dist='default'>home/httpd/cgi-bin/barcode.gif</target>
+<source>loncom/interface/filecategories.tab</source>
+<target dist='default'>home/httpd/lonTabs/filecategories.tab</target>
+<categoryname>static conf</categoryname>
+<description>
+Descriptive list of file extensions and broad categorization.
+</description>
+</file>
+<file>
+<source>loncom/cgi/barcode.png</source>
+<target dist='default'>home/httpd/cgi-bin/barcode.png</target>
 <categoryname>script</categoryname>
 <description>
 Dynamically outputs a barcode based on a CGI passed encode=BARCODEVALUE
@@ -635,6 +858,38 @@ parameter.
 </description>
 </file>
 <file>
+<source>loncom/cgi/decompress.pl</source>
+<target dist='default'>home/httpd/cgi-bin/decompress.pl</target>
+<categoryname>script</categoryname>
+<description>
+Decompresses an archive into its files inside of the construction space
+</description>
+</file>
+<file>
+<source>loncom/cgi/takeoffline.pl</source>
+<target dist='default'>home/httpd/cgi-bin/takeoffline.pl</target>
+<categoryname>script</categoryname>
+<description>
+Take machine offline
+</description>
+</file>
+<file>
+<source>loncom/cgi/takeonline.pl</source>
+<target dist='default'>home/httpd/cgi-bin/takeonline.pl</target>
+<categoryname>script</categoryname>
+<description>
+Take machine online
+</description>
+</file>
+<file>
+<source>loncom/cgi/thumbnail.gif</source>
+<target dist='default'>home/httpd/cgi-bin/thumbnail.gif</target>
+<categoryname>script</categoryname>
+<description>
+Produces a thumbnail image of the url given
+</description>
+</file>
+<file>
 <source>loncom/cgi/clusterstatus.pl</source>
 <target dist='default'>home/httpd/cgi-bin/clusterstatus.pl</target>
 <categoryname>script</categoryname>
@@ -643,8 +898,40 @@ utility cgi script to view status of clu
 </description>
 </file>
 <file>
-<source>loncom/cgi/graph.gif</source>
-<target dist='default'>home/httpd/cgi-bin/graph.gif</target>
+<source>loncom/cgi/translator.pl</source>
+<target dist='default'>home/httpd/cgi-bin/translator.pl</target>
+<categoryname>script</categoryname>
+<description>
+utility cgi script to enter translations
+</description>
+</file>
+<file>
+<source>loncom/build/system_dependencies/perltest.pl</source>
+<target dist='default'>home/httpd/cgi-bin/perltest.pl</target>
+<categoryname>script</categoryname>
+<description>
+utility cgi script to view status of perl modules
+</description>
+</file>
+<file>
+<source>loncom/build/system_dependencies/cpan_distributions.txt</source>
+<target dist='default'>home/httpd/cgi-bin/cpan_distributions.txt</target>
+<categoryname>interface file</categoryname>
+<description>
+utility cgi script to view status of perl modules
+</description>
+</file>
+<file>
+  <source>loncom/cgi/loncgi.pm</source>
+  <target dist='default'>home/httpd/lib/perl/LONCAPA/loncgi.pm</target>
+  <categoryname>system file</categoryname>
+  <description>
+      Provides a common interface to LON-CAPA cookies and environment.
+  </description>
+</file>
+<file>
+<source>loncom/cgi/graph.png</source>
+<target dist='default'>home/httpd/cgi-bin/graph.png</target>
 <categoryname>script</categoryname>
 <description>
 Dynamically outputs a graph especially for lonstatistics.pm.
@@ -679,6 +966,14 @@ Dynamically outputs X-Y plots with point
 </description>
 </file>
 <file>
+<source>loncom/cgi/imagechoice.pl</source>
+<target dist='default'>home/httpd/cgi-bin/imagechoice.pl</target>
+<categoryname>script</categoryname>
+<description>
+Helper to select image coordinates in writing homework involving images.
+</description>
+</file>
+<file>
 <source>loncom/interface/printout.pl</source>
 <target dist='default'>home/httpd/cgi-bin/printout.pl</target>
 <categoryname>script</categoryname>
@@ -709,6 +1004,48 @@ coil,loop,field,magnetic
 and simply prints this text-only (no markup) to the browser
 </description>
 </file>
+<file>
+<source>loncom/cgi/metadata_harvest.pl</source>
+<target dist='default'>home/httpd/cgi-bin/metadata_harvest.pl</target>
+<categoryname>script</categoryname>
+<description>
+a cgi-script (not mod_perl), which contacts MySQL and pulls
+out all records in "|"-separated format.
+To be used by very simple harvesting engines.
+</description>
+</file>
+<file>
+<source>loncom/homework/simpleproblem.problem</source>
+<target dist='default'>home/httpd/html/res/lib/templates/simpleproblem.problem</target>
+<categoryname>interface file</categoryname>
+<description>
+Generic resource for DOCS "Simple Problem"
+</description>
+</file>
+<file>
+<source>loncom/homework/simpleproblem.problem.meta</source>
+<target dist='default'>home/httpd/html/res/lib/templates/simpleproblem.problem.meta</target>
+<categoryname>interface file</categoryname>
+<description>
+Meta file for generic resource for DOCS "Simple Problem"
+</description>
+</file>
+<file>
+<source>loncom/homework/templates/examupload.problem</source>
+<target dist='default'>home/httpd/html/res/lib/templates/examupload.problem</target>
+<categoryname>interface file</categoryname>
+<description>
+Generic resource for score upload
+</description>
+</file>
+<file>
+<source>loncom/homework/templates/examupload.problem.meta</source>
+<target dist='default'>home/httpd/html/res/lib/templates/examupload.problem.meta</target>
+<categoryname>interface file</categoryname>
+<description>
+Meta file for generic resource for score upload
+</description>
+</file>
 <fileglob>
 <glob>*.*</glob>
 <sourcedir>loncom/homework/templates/</sourcedir>
@@ -723,12 +1060,22 @@ blank.library;
 blank.library.meta;
 blank.problem;
 blank.problem.meta;
-formula.problem;
-formula.problem.meta;
+ClickImageExample.problem;
+ClickImageExample.problem.meta;
+Essay.problem;
+Essay.problem.meta;
+examupload.problem;
+examupload.problem.meta;
+man1.jpg;
+man1.jpg.meta;
 numerical.problem;
 numerical.problem.meta;
+Plot.problem;
+Plot.problem.meta;
 RadioResponse.problem;
 RadioResponse.problem.meta;
+RandomLabelExample.problem;
+RandomLabelExample.problem.meta;
 SelectFromOptions-4ConceptGoups.problem;
 SelectFromOptions-4ConceptGoups.problem.meta;
 SelectFromOptions-5ConceptGoups.problem;
@@ -743,10 +1090,16 @@ SelectFromOptions-Simple.problem;
 SelectFromOptions-Simple.problem.meta;
 script.library;
 script.library.meta;
-SimpleStringResponse.problem;
-SimpleStringResponse.problem.meta;
+SimpleFormula.problem;
+SimpleFormula.problem.meta;
 StringResponse.problem;
-StringResponse.problem.meta
+StringResponse.problem.meta;
+SimpleMatching.problem;
+SimpleMatching.problem.meta;
+SimpleRank.problem;
+SimpleRank.problem.meta;
+SimpleTrueFalse.problem;
+SimpleTrueFalse.problem.meta
 </filenames>
 </fileglob>
 <file>
@@ -770,8 +1123,8 @@ Built from Glabel.java.  Still working o
 </note>
 </file>
 <file>
-<source>loncom/interface/default.assesscalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.assesscalc
+<source>loncom/interface/spreadsheet/default_assesscalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_assesscalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -779,8 +1132,8 @@ Default spreadsheet for individual asses
 </description>
 </file>
 <file>
-<source>loncom/interface/default.studentcalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.studentcalc
+<source>loncom/interface/spreadsheet/default_studentcalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_studentcalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -788,8 +1141,8 @@ Default spreadsheet for assessment of st
 </description>
 </file>
 <file>
-<source>loncom/interface/default.classcalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.classcalc
+<source>loncom/interface/spreadsheet/default_classcalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_classcalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -814,15 +1167,23 @@ Descriptive list of abbreviations used i
 and privileges available in the network with function
 </description>
 </file>
-<file>
+<file type="private">
 <source>loncom/hosts.tab</source>
 <target dist='default'>home/httpd/lonTabs/hosts.tab</target>
-<categoryname>static conf</categoryname>
+<categoryname>www static conf</categoryname>
 <description>
 List of all machines in the LON-CAPA network.  Relates <tt>lonHostID</tt> to
 <tt>lonDefDomain</tt> and <u>IP address</u>.
 </description>
 </file>
+<file type="private">
+<source>loncom/domain.tab</source>
+<target dist='default'>home/httpd/lonTabs/domain.tab</target>
+<categoryname>www static conf</categoryname>
+<description>
+List of all domains in the LON-CAPA network. Lists the name name of the domain and any default authentication.
+</description>
+</file>
 <file>
 <source>loncom/spare.tab</source>
 <target dist='default'>home/httpd/lonTabs/spare.tab</target>
@@ -846,16 +1207,15 @@ in <tt>access.conf</tt>
 <file>
 <source>loncom/htpasswd</source>
 <target dist='default'>home/httpd/lonTabs/htpasswd</target>
-<categoryname>conf</categoryname>
+<categoryname>static conf</categoryname>
 <description>
 Basic auth password to access /lon-status and /server-status
 </description>
 </file>
 <file>
 <source>loncom/smb.conf</source>
-<target dist='default'>etc/smb.conf</target>
-<target dist='redhat7.1'>etc/samba/smb.conf</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/smb.conf</target>
+<categoryname>static conf</categoryname>
 <description>
 configuration file to make LON-CAPA server file space accessible to network
 neighborhood
@@ -863,8 +1223,8 @@ neighborhood
 </file>
 <file>
 <source>loncom/ntp.conf</source>
-<target dist='default'>etc/ntp.conf</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/ntp.conf</target>
+<categoryname>static conf</categoryname>
 <description>
 which NTP server to contact for information (XNTP3 standard)
 </description>
@@ -888,6 +1248,31 @@ Batch script for updating SQL metadata d
 </description>
 </file>
 <file>
+<source>loncom/metadata_database/cleanup_database.pl</source>
+<target dist='default'>home/httpd/perl/cleanup_database.pl</target>
+<categoryname>script</categoryname>
+<description>
+Batch script for removing temporary tables from the SQL metadata database.
+</description>
+</file>
+<file>
+<source>loncom/misc/cleanup_prtspool.pl</source>
+<target dist='default'>home/httpd/perl/cleanup_prtspool.pl</target>
+<categoryname>script</categoryname>
+<description>
+Batch script for removing files not accessed within 24 hours from the 
+/home/httpd/prtspool directory.
+</description>
+</file>
+<file>
+<source>loncom/lonhttpd</source>
+<target dist='default'>home/httpd/perl/lonhttpd</target>
+<categoryname>script</categoryname>
+<description>
+Small fry httpd on port 8080
+</description>
+</file>
+<file>
 <source>loncom/lonc</source>
 <target dist='default'>home/httpd/perl/lonc</target>
 <categoryname>script</categoryname>
@@ -901,7 +1286,8 @@ proxy server
 <categoryname>doc</categoryname>
 <description>man page for lonc</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../lonc > ../../doc/man/lonc.1 && echo 'manifying lonc'
+loncom/build/pod2man.sh ../lonc &gt; ../../doc/man/lonc.1 &amp;&amp; \
+echo 'manifying lonc'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -914,7 +1300,8 @@ loncom/build/pod2man.sh ../lonc > ../../
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonc</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../lonc > ../../doc/scripts/lonc.html && echo 'pod2html lonc'
+loncom/build/pod2html.sh ../lonc &gt; ../../doc/scripts/lonc.html &amp;&amp; \
+echo 'pod2html lonc'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -931,7 +1318,7 @@ It accepts and processes incoming reques
 on the network.  lond's functionality is self-contained in the sense
 that it does not reference (import, require, use) any other file
 described in this document.  There are only 15 subroutines in this
-script, however the <TT>make_new_child</TT> subroutine is quite
+script, however the <tt>make_new_child</tt> subroutine is quite
 complex since it parses and responds about 29 different types of 
 network requests (i.e. enc, ping, pong, ekey, load, auth, passwd,
 makeuser, home, update, unsub, sub, log, put, rolesput, get, eget,
@@ -945,7 +1332,8 @@ tmpput, tmpget, and ls).
 <categoryname>doc</categoryname>
 <description>man page for lond</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../lond > ../../doc/man/lond.1 && echo 'manifying lond'
+loncom/build/pod2man.sh ../lond &gt; ../../doc/man/lond.1 &amp;&amp; \
+echo 'manifying lond'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -958,7 +1346,8 @@ loncom/build/pod2man.sh ../lond > ../../
 <categoryname>doc</categoryname>
 <description>POD-derived page for lond</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../lond > ../../doc/scripts/lond.html && echo 'pod2html lond'
+loncom/build/pod2html.sh ../lond &gt; ../../doc/scripts/lond.html &amp;&amp; \
+echo 'pod2html lond'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -966,12 +1355,24 @@ loncom/build/pod2html.sh ../lond > ../..
 </dependencies>
 </file>
 <file>
+<source>loncom/build/CHECKRPMS</source>
+<target dist='default'>home/httpd/cgi-bin/CHECKRPMS</target>
+<categoryname>script</categoryname>
+<description>CGI script that checks status of RPMs</description>
+</file>
+<file>
 <source>loncom/cgi/loncron.pl</source>
 <target dist='default'>home/httpd/cgi-bin/loncron.pl</target>
 <categoryname>script</categoryname>
 <description>CGI script that starts and pipes output of loncron</description>
 </file>
 <file>
+<source>loncom/cgi/userstatus.pl</source>
+<target dist='default'>home/httpd/cgi-bin/userstatus.pl</target>
+<categoryname>script</categoryname>
+<description>CGI script that shows users currently on machine</description>
+</file>
+<file>
 <source>loncom/loncron</source>
 <target dist='default'>home/httpd/perl/loncron</target>
 <categoryname>script</categoryname>
@@ -989,7 +1390,8 @@ loncom/build/pod2html.sh ../lond > ../..
 <categoryname>doc</categoryname>
 <description>man page for lonsql</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../lonsql > ../../doc/man/lonsql.1 && echo 'manifying lonsql'
+loncom/build/pod2man.sh ../lonsql &gt; ../../doc/man/lonsql.1 &amp;&amp; \
+echo 'manifying lonsql'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1002,7 +1404,8 @@ loncom/build/pod2man.sh ../lonsql > ../.
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonsql</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../lonsql > ../../doc/scripts/lonsql.html && echo 'pod2html lonsql'
+loncom/build/pod2html.sh ../lonsql &gt; ../../doc/scripts/lonsql.html &amp;&amp; \
+echo 'pod2html lonsql'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1039,6 +1442,17 @@ new user.
 <status>being updated</status>
 </file>
 <file>
+<source>loncom/lchtmldir</source>
+<target dist='default'>home/httpd/perl/lchtmldir</target>
+<categoryname>setuid script</categoryname>
+<description>
+Manages the file system ramifications of adding author mode to a user. 
+If necessary a public_html diretory is added, permissions and ownership are
+set according to the user's authentication mode.
+</description>
+<status>New file</status>
+</file>
+<file>
 <source>loncom/lcuserdel</source>
 <target dist='default'>home/httpd/perl/lcuserdel</target>
 <categoryname>setuid script</categoryname>
@@ -1077,6 +1491,22 @@ GNU General Public License.  Long live t
 </description>
 </file>
 <file>
+<source>loncom/license/httpi.license</source>
+<target dist='default'>home/httpd/html/adm/httpi.license</target>
+<categoryname>interface file</categoryname>
+<description>
+HTTPi webserver license
+</description>
+</file>
+<file>
+<source>loncom/license/httpi.readme</source>
+<target dist='default'>home/httpd/html/adm/httpi.readme</target>
+<categoryname>interface file</categoryname>
+<description>
+HTTPi webserver readme 
+</description>
+</file>
+<file>
 <source>loncom/license/about.html</source>
 <target dist='default'>home/httpd/html/adm/about.html</target>
 <categoryname>interface file</categoryname>
@@ -1102,6 +1532,31 @@ Interface file for responding to imprope
 </description>
 </file>
 <file>
+<source>loncom/html/adm/notinit.html</source>
+<target dist='default'>home/httpd/html/adm/notinit.html</target>
+<categoryname>interface file</categoryname>
+<description>
+Interface file for responding to accessing uploaded resources without
+re-initializing course.
+</description>
+</file>
+<file>
+<source>loncom/html/adm/overloaded.txt</source>
+<target dist='default'>home/httpd/html/adm/overloaded.txt</target>
+<categoryname>interface file</categoryname>
+<description>
+Interface file for responding to overload situations.
+</description>
+</file>
+<file>
+<source>loncom/html/adm/loginproblems.html</source>
+<target dist='default'>home/httpd/html/adm/loginproblems.html</target>
+<categoryname>interface file</categoryname>
+<description>
+Help page for login problems.
+</description>
+</file>
+<file>
 <source>loncom/xml/physnet.sty</source>
 <target dist='default'>home/httpd/html/res/adm/includes/physnet.sty</target>
 <categoryname>static conf</categoryname>
@@ -1111,14 +1566,15 @@ The relevant conditions and metadata to
 </file>
 <file>
 <source>loncom/homework/lectureonline.sty</source>
-<target dist='default'>home/httpd/html/res/adm/includes/lectureonline.sty</target>
+<target dist='default'>home/httpd/html/res/adm/includes/lectureonline.sty
+</target>
 <categoryname>static conf</categoryname>
 <description>
 The relevant conditions and metadata to attach to LectureOnline-specific tags.
 </description>
 </file>
 <file>
-<source>loncom/misc/un_keyword.tab</source>
+<source>loncom/thesaurus/un_keyword.tab</source>
 <target dist='default'>home/httpd/html/res/adm/includes/un_keyword.tab</target>
 <categoryname>conf</categoryname>
 <description>
@@ -1127,6 +1583,14 @@ content.
 </description>
 </file>
 <file>
+<source>loncom/homework/scantronformat.tab</source>
+<target dist='default'>home/httpd/lonTabs/scantronformat.tab</target>
+<categoryname>conf</categoryname>
+<description>
+Different configs for scantron input files.
+</description>
+</file>
+<file>
 <source>loncom/publisher/packages.tab</source>
 <target dist='default'>home/httpd/lonTabs/packages.tab</target>
 <categoryname>static conf</categoryname>
@@ -1172,6 +1636,105 @@ Edit handler for rat maps; TeX content h
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/londocs.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/londocs.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for course documents
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonchat.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonchat.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for chat
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonchatfetch.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonchatfetch.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for periodically fetch new lines of chat
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonannounce.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonannounce.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up announcements and calendar
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonsyllabus.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonsyllabus.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up syllabus
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/homework/lonsimpleproblemedit.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonsimpleproblemedit.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to set parameters for simple homework problems
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonsimplepage.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonsimplepage.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up simple page
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonpickstudent.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonpickstudent.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to pick a student from classlist
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonpickcourse.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonpickcourse.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to pick a courseid from a list of courses
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonbulletin.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonbulletin.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up bulletin board
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonaboutme.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonaboutme.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up personal info
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/publisher/loncfile.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/loncfile.pm</target>
 <categoryname>handler</categoryname>
@@ -1182,6 +1745,464 @@ construction space menu.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonhelp.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonhelp.pm</target>
+<categoryname>handler</categoryname>
+<description>
+The .tex file help handler.
+</description>
+<status>works/unverified</status>
+<build trigger='always run'>
+loncom/html/adm/help/buildMakeWrapper
+</build>
+<dependencies>
+Makefile;
+buildMakeWrapper
+</dependencies>
+</file>
+<file>
+<source>loncom/html/adm/help/abouthelp.html</source>
+<target dist='default'>home/httpd/html/adm/help/abouthelp.html</target>
+<categoryname>interface file</categoryname>
+<description>
+Index file for the help system
+</description>
+</file>
+<file>
+<source>doc/help/author.manual.access.tex</source>
+<target dist='default'>home/httpd/html/adm/help/tex/author.manual.access.tex
+</target>
+<categoryname>interface file</categoryname>
+<description>
+The pseudo-LaTeX file to allow people to read the author's manual online, with
+a somewhat clumsy interface.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/course.manual.access.tex</source>
+<target dist='default'>home/httpd/html/adm/help/tex/course.manual.access.tex
+</target>
+<categoryname>interface file</categoryname>
+<description>
+The pseudo-LaTeX file to allow people to read the course administrator's
+manual online, with a somewhat clumsy interface.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/author.manual.ps</source>
+<target dist='default'>home/httpd/html/adm/help/author.manual.ps</target>
+<categoryname>interface file</categoryname>
+<description>
+The postscript Author's Manual
+</description>
+<status>works/unverified</status>
+<dependencies>
+doc/help/author.manual.texxml;
+doc/help/latexSplitter.py;
+doc/help/rebuildLabelHash.pl;
+doc/help/render.texxml.pl;
+doc/help/simpleEdit.py;
+doc/help/texxml2indextex.pl;
+doc/help/texxml2latex.pl;
+loncom/build/buildHelp.sh;
+loncom/build/help_graphics_converter.pl
+</dependencies>
+</file>
+<file>
+<source>doc/help/author.manual.pdf</source>
+<target dist='default'>home/httpd/html/adm/help/author.manual.pdf</target>
+<categoryname>handler</categoryname>
+<description>
+The PDF Author's Manual
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/course.manual.ps</source>
+<target dist='default'>home/httpd/html/adm/help/course.manual.ps</target>
+<categoryname>interface file</categoryname>
+<description>
+The postscript Course Manual
+</description>
+<status>works/unverified</status>
+<dependencies>
+doc/help/course.manual.texxml;
+doc/help/latexSplitter.py;
+doc/help/rebuildLabelHash.pl;
+doc/help/render.texxml.pl;
+doc/help/simpleEdit.py;
+doc/help/texxml2indextex.pl;
+doc/help/texxml2latex.pl;
+loncom/build/buildHelp.sh;
+loncom/build/help_graphics_converter.pl
+</dependencies>
+</file>
+<file>
+<source>doc/help/course.manual.pdf</source>
+<target dist='default'>home/httpd/html/adm/help/course.manual.pdf</target>
+<categoryname>interface file</categoryname>
+<description>
+The PDF Course Manual
+</description>
+<status>works/unverified</status>
+</file>
+<fileglob>
+<glob>*.*</glob>
+<sourcedir>loncom/html/adm/help/gif/</sourcedir>
+<targetdir dist='default'>
+home/httpd/html/adm/help/gif/</targetdir>
+<categoryname>interface file</categoryname>
+<description>
+Gif files for the help system
+</description>
+<filenames>
+authorRemote.gif;
+constructionSpace.gif;
+constructionSpaceForPublishing.gif;
+creatingANewCourse.gif;
+creatingNewProblemResource.gif;
+dynamic_piecewise.gif;
+dynamic_piecewise2.gif;
+dynamic_plot.gif;
+dynamic_plot2.gif;
+formulaResponse.gif;
+login.gif;
+lonhelpheader.gif;
+mainCourseDocuments.gif;
+mapAdvancedEditorNew.gif;
+mapClickedStart.gif;
+mapEditFirstClick.gif;
+mapEditInitial.gif;
+mapEditingButton.gif;
+mapEditorDirectoryBrowser.gif;
+mapEditorResourceChosen.gif;
+mapEditorSelection.gif;
+mapInsertResource.gif;
+mapNewResource.gif;
+mapSecondWindowSecondResource.gif;
+mapSimpleEditor.gif;
+mapStraightened.gif;
+mapTwoResources.gif;
+numericalResponse1.gif;
+numericalResponseEditor.gif;
+numericalResponseSlopeProblem.gif;
+numericalResponseVarInText.gif;
+optionResponseEditing.gif;
+optionResponseProblem.gif;
+publishMetadata.gif;
+radioResponse2.gif;
+radioResponseHint.gif;
+smallHelp.gif;
+spreadsheet_hierarchy.gif;
+stringResponseEditor.gif;
+studentInterface.gif
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.*</glob>
+<sourcedir>loncom/html/adm/help/eps/</sourcedir>
+<targetdir dist='default'>
+home/httpd/html/adm/help/eps/</targetdir>
+<categoryname>interface file</categoryname>
+<description>
+EPS files for the help system
+</description>
+<filenames>
+authorRemote.eps;
+constructionSpace.eps;
+constructionSpaceForPublishing.eps;
+creatingANewCourse.eps;
+creatingNewProblemResource.eps;
+dynamic_piecewise.eps;
+dynamic_piecewise2.eps;
+dynamic_plot.eps;
+dynamic_plot2.eps;
+formulaResponse.eps;
+lonhelpheader.eps;
+login.eps;
+mainCourseDocuments.eps;
+mapAdvancedEditorNew.eps;
+mapClickedStart.eps;
+mapEditFirstClick.eps;
+mapEditInitial.eps;
+mapEditingButton.eps;
+mapEditorDirectoryBrowser.eps;
+mapEditorResourceChosen.eps;
+mapEditorSelection.eps;
+mapInsertResource.eps;
+mapNewResource.eps;
+mapSecondWindowSecondResource.eps;
+mapSimpleEditor.eps;
+mapStraightened.eps;
+mapTwoResources.eps;
+numericalResponse1.eps;
+numericalResponseEditor.eps;
+numericalResponseSlopeProblem.eps;
+numericalResponseVarInText.eps;
+optionResponseEditing.eps;
+optionResponseProblem.eps;
+publishMetadata.eps;
+radioResponse2.eps;
+radioResponseHint.eps;
+smallHelp.eps;
+spreadsheet_hierarchy.eps;
+stringResponseEditor.eps;
+studentInterface.eps
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.*</glob>
+<sourcedir>loncom/html/adm/help/tex/</sourcedir>
+<targetdir dist='default'>
+home/httpd/html/adm/help/tex/</targetdir>
+<categoryname>interface file</categoryname>
+<description>
+Tex files for the help system
+</description>
+<filenames>
+About_Authors_Manual.tex;
+About_Communication.tex;
+About_Developers_Manual.tex;
+About_Numerical_and_Formula_Response.tex;
+Ambiguous_Reference.tex;
+Analyze_Problem.tex;
+Annotation.tex;
+Authentication.tex;
+Author_LON-CAPA_Introduction.tex;
+Author_Manual_Title_Page.tex;
+Author_Numerical_and_Formula.tex;
+Author_Remote_Control.tex;
+Authoring_Adding_Pictures.tex;
+Authoring_DataResponse.tex;
+Authoring_Dynamic_Plot.tex;
+Authoring_ExternalResponse.tex;
+Authoring_Foil_Structure_Tags.tex;
+Authoring_HTML_vs_Tex.tex;
+Authoring_Hint_Tags.tex;
+Authoring_ImageResponse.tex;
+Authoring_Input_Tags.tex;
+Authoring_Internal_Tags.tex;
+Authoring_M_Tag.tex;
+Authoring_NumericalResponse.tex;
+Authoring_OptionResponse.tex;
+Authoring_Output_Tags.tex;
+Authoring_Pictures_EPS.tex;
+Authoring_Piecewise_Plot.tex;
+Authoring_RadiobuttonResponse.tex;
+Authoring_Response_Attributes.tex;
+Authoring_Response_Tag_Intro.tex;
+Authoring_Responseparam_Parameter.tex;
+Authoring_Scripting_Tags.tex;
+Authoring_Structure_Tags.tex;
+Authoring_XML_Intro.tex;
+Bookmarks.tex;
+Bugzilla.tex;
+CAPA_LON-CAPA_function_diffs.tex;
+Caching.tex;
+Calendar_Add_Announcement.tex;
+Calendar_Remove_Announcement.tex;
+Calling_Functions.tex;
+Cascading_Parameters.tex;
+Change_Colors.tex;
+Change_Password.tex;
+Chart_Description.tex;
+Chart_Output_Data.tex;
+Chart_Output_Formats.tex;
+Chatting.tex;
+Coauthor.tex;
+Construction_Space_Overview.tex;
+Course_Add_Other.tex;
+Course_Add_Student.tex;
+Course_Broadcast_Message.tex;
+Course_Change_Privileges.tex;
+Course_Chart_To_Excel.tex;
+Course_Chat.tex;
+Course_Convert_To_CSV.tex;
+Course_Create_Class_List.tex;
+Course_Critical_Message.tex;
+Course_Deleting.tex;
+Course_Disable_Discussion.tex;
+Course_Discussion_Board.tex;
+Course_Drop_Student.tex;
+Course_Edit_Content.tex;
+Course_Editing_Custom_Roles.tex;
+Course_Extending_Due_Dates.tex;
+Course_Face_To_Face_Records.tex;
+Course_Feedback_Addresses.tex;
+Course_Homework_Performance_Overview.tex;
+Course_Manual_Title_Page.tex;
+Course_Manually_Grade_Problem.tex;
+Course_Maximum_Collaborators.tex;
+Course_Message_Access.tex;
+Course_Modify_Student_Data.tex;
+Course_Parameter_Levels.tex;
+Course_Problem_Weight.tex;
+Course_Set_Start_End_Date.tex;
+Course_Setting_Parameters.tex;
+Course_Student_Grade_Override.tex;
+Course_Student_Work.tex;
+Course_Toplevel_Seq.tex;
+Course_User_Evaluation.tex;
+Course_User_Parameter.tex;
+Course_View_Class_List.tex;
+Create_Course.tex;
+Creating_A_Course_Intro.tex;
+Creating_New_Content_Pages.tex;
+Creating_Online_Problems.tex;
+Creating_Radio_Response_Problems.tex;
+Developer_Manual_Title_Page.tex;
+Developer_Tutorial.tex;
+Docs_About_Bulletin_Board.tex;
+Docs_About_My_Personal_Info.tex;
+Docs_About_Simple_Page.tex;
+Docs_About_Syllabus.tex;
+Docs_Adding_Course_Doc.tex;
+Docs_Adding_External_Resource.tex;
+Docs_Adding_Folders.tex;
+Docs_Adding_Syllabus.tex;
+Docs_Alternatives.tex;
+Docs_Creating_From_Template.tex;
+Docs_Editing_Templated_Pages.tex;
+Docs_Importing_LON-CAPA_Resource.tex;
+Docs_Load_Map.tex;
+Docs_Main_Course_Documents.tex;
+Docs_Navigate_Content.tex;
+Docs_Overview.tex;
+Docs_Score_Upload_Form.tex;
+Docs_Supplemental.tex;
+Docs_Uploading_From_Harddrive.tex;
+Finding_Resources.tex;
+Foils.tex;
+Formula_Response_Adv_Intro.tex;
+Formula_Response_Example.tex;
+Formula_Response_Limitations.tex;
+Formula_Response_Problems.tex;
+Formula_Response_Sampling.tex;
+Formula_Tolerance.tex;
+General_Intro.tex;
+Greek_Symbols.tex;
+Guts_Apache.tex;
+Guts_Apache_Env.tex;
+Guts_Apache_Modules.tex;
+Guts_Authentication.tex;
+Guts_Authoring.tex;
+Guts_Coding_Guidelines.tex;
+Guts_Course_Dir.tex;
+Guts_User_Dir.tex;
+How_To_Edit_Existing_Content_Pages.tex;
+Latex_Footer.tex;
+Latex_Header.tex;
+Leaving_Feedback.tex;
+Login_To_LON-CAPA.tex;
+Metadata_Description.tex;
+Navmap_Host_Down.tex;
+Numerical_Response_Advanced_Example.tex;
+Numerical_Response_Format.tex;
+Numerical_Response_Intro.tex;
+Numerical_Response_Introduction.tex;
+Numerical_Response_Parts_A.tex;
+Numerical_Response_Parts_B.tex;
+Numerical_Response_Problems.tex;
+Numerical_Response_Randomization.tex;
+Numerical_Response_Simple_Example.tex;
+Numerical_Response_Tutorial_A.tex;
+Numerical_Response_Units.tex;
+Option_Response_Concept_Group_Example.tex;
+Option_Response_Matching_Example.tex;
+Option_Response_Problem_Creation.tex;
+Option_Response_Problem_Figure.tex;
+Option_Response_Problem_Parts.tex;
+Option_Response_Problems.tex;
+Option_Response_Simple.tex;
+Other_Symbols.tex;
+Part_Tag_Edit_Help.tex;
+Personal_Info_Page.tex;
+Physical_Units.tex;
+Prefs_Forwarding.tex;
+Prefs_Screen_Name_Nickname.tex;
+Print_Resource.tex;
+Problem_Editor_Testing_Area.tex;
+Problem_Editor_XML_Index.tex;
+Problem_LON-CAPA_Functions.tex;
+Problem_Types.tex;
+Publishing_A_Resource.tex;
+Publishing_Author_Tutorial_Segue.tex;
+Publishing_Copyright.tex;
+Publishing_Intro.tex;
+Publishing_Keywords.tex;
+Quick_Grades_Possibly_Correct.tex;
+Radio_Response_Problems.tex;
+Radio_Response_Randomization.tex;
+Ranking_Problems.tex;
+Receipt.tex;
+Resource_Discussion.tex;
+Resource_Types.tex;
+Roles_About.tex;
+Script_Functions.tex;
+Script_Tutorial_Intro.tex;
+Script_Variables.tex;
+Scripting_Help.tex;
+Sending_Email.tex;
+Sequence_Advanced_Editor_Creation.tex;
+Sequence_Definition.tex;
+Sequence_Editor_Selection.tex;
+Sequence_Page_Maps.tex;
+Sequence_Simple_Editor_Creation.tex;
+Sequence_Top-Level.tex;
+Significant_Figures.tex;
+Spreadsheet_About.tex;
+Spreadsheet_Calculation.tex;
+Spreadsheet_Calculation_Time.tex;
+Spreadsheet_Cell_Editing.tex;
+Spreadsheet_Editing.tex;
+Spreadsheet_Export_Row.tex;
+Spreadsheet_Files.tex;
+Spreadsheet_Functions.tex;
+Spreadsheet_Hierarchy.tex;
+Spreadsheet_HowTo_Assessments.tex;
+Spreadsheet_HowTo.tex;
+Spreadsheet_Layout.tex;
+Spreadsheet_Levels.tex;
+Spreadsheet_Max_Depth_Exceeded.tex;
+Spreadsheet_Parms.tex;
+Spreadsheet_Problem_Weight.tex;
+Spreadsheet_Referencing_Cells.tex;
+Spreadsheet_Referencing_Parameters.tex;
+Spreadsheet_Row_Numbers.tex;
+Spreadsheet_Student_View.tex;
+Spreadsheet_Student_Visible.tex;
+Spreadsheet_Template_Row.tex;
+Spreadsheet_Ternary_Operator.tex;
+Spreadsheet_Tries.tex;
+String_Response_Problem_Creation.tex;
+String_Response_Problems.tex;
+Syllabus_ExtLink.tex;
+Syllabus_URLs.tex;
+Tolerance.tex;
+Uploaded_Templates_PublicView.tex;
+Uploaded_Templates_TextBoxes.tex;
+Variable_Naming_Conventions.tex;
+Variable_Tutorial_A.tex;
+Variables_in_Scripts.tex;
+Variables_in_the_Answer_Block.tex;
+Variables_in_the_Text_Block.tex;
+What_Is_LON-CAPA.tex;
+Why_LON-CAPA.tex;
+all_functions_table.tex;
+</filenames>
+</fileglob>
+<file>
+<source>loncom/html/adm/help/fragmentLabels.gdbm</source>
+<target dist='default'>home/httpd/html/adm/help/fragmentLabels.gdbm</target>
+<categoryname>interface file</categoryname>
+<description>
+A gdbm file containing a label->tex file hash.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/lonstatistics.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonstatistics.pm</target>
 <categoryname>handler</categoryname>
@@ -1191,6 +2212,56 @@ Handler to show statistics on solving LO
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/statistics/lonproblemstatistics.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonproblemstatistics.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+The module that generate the html for the Problem Statistics web pages.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/statistics/lonpercentage.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonpercentage.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+The module that generate the html for the Percentage graph web pages.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/statistics/lonproblemanalysis.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonproblemanalysis.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+This module provides detailed analysis and raw data for submissions of various problem types.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/statistics/lonsubmissiontimeanalysis.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonsubmissiontimeanalysis.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+This module produces plots of the times of students attempts on an assessment.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/statistics/lonstudentassessment.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonstudentassessment.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+The module that generate the html for the Student Assessment/Chart web pages.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/publisher/londiff.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/londiff.pm</target>
 <categoryname>handler</categoryname>
@@ -1200,6 +2271,15 @@ Handler to show difference between two f
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/publisher/lonrights.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonrights.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to show and edit custom distribution rights
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/publisher/lonupload.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonupload.pm</target>
 <categoryname>handler</categoryname>
@@ -1214,7 +2294,8 @@ Handler to upload files through browser
 <categoryname>doc</categoryname>
 <description>man page for lonupload.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../publisher/lonupload.pm > ../../doc/man/Apache__lonupload.3 && echo 'manifying lonupload.pm'
+loncom/build/pod2man.sh ../publisher/lonupload.pm &gt; \
+../../doc/man/Apache__lonupload.3 &amp;&amp; echo 'manifying lonupload.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1222,12 +2303,15 @@ loncom/build/pod2man.sh ../publisher/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonupload.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonupload.html</target>
+<source>doc/lib/perl/Apache/lonupload.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonupload.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonupload.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../publisher/lonupload.pm > ../../doc/api/Apache/lonupload.html && echo 'pod2html lonupload.pm'
+loncom/build/pod2html.sh ../publisher/lonupload.pm &gt; \
+../../doc/lib/perl/Apache/lonupload.html &amp;&amp; \
+echo 'pod2html lonupload.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1257,7 +2341,8 @@ Handler to evaluate externally graded re
 <target dist='default'>home/httpd/lib/perl/Apache/loncapagrade.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Handler to evaluate externally graded responses.
+Holds results and defines
+tag handlers needed by externalresponse.pm
 </description>
 <status>works/unverified</status>
 </file>
@@ -1270,12 +2355,21 @@ Handler to publish directories.
 </description>
 </file>
 <file>
+<source>loncom/publisher/lonunauthorized.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonunauthorized.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to explain failed contruction space access.
+</description>
+</file>
+<file>
 <source>doc/man/Apache__lonpubdir.3</source>
 <target dist='default'>usr/man/man3/Apache::lonpubdir.3</target>
 <categoryname>doc</categoryname>
 <description>man page for lonpubdir.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../publisher/lonpubdir.pm > ../../doc/man/Apache__lonpubdir.3 && echo 'manifying lonpubdir.pm'
+loncom/build/pod2man.sh ../publisher/lonpubdir.pm &gt; \
+../../doc/man/Apache__lonpubdir.3 &amp;&amp; echo 'manifying lonpubdir.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1283,12 +2377,15 @@ loncom/build/pod2man.sh ../publisher/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonpubdir.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonpubdir.html</target>
+<source>doc/lib/perl/Apache/lonpubdir.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonpubdir.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonpubdir.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../publisher/lonpubdir.pm > ../../doc/api/Apache/lonpubdir.html && echo 'pod2html lonpubdir.pm'
+loncom/build/pod2html.sh ../publisher/lonpubdir.pm &gt; \
+../../doc/lib/perl/Apache/lonpubdir.html &amp;&amp; \
+echo 'pod2html lonpubdir.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1310,7 +2407,8 @@ Handler to retrieve old versions from re
 <categoryname>doc</categoryname>
 <description>man page for lonretrieve.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../publisher/lonretrieve.pm > ../../doc/man/Apache__lonretrieve.3 && echo 'manifying lonretrieve.pm'
+loncom/build/pod2man.sh ../publisher/lonretrieve.pm &gt; \
+../../doc/man/Apache__lonretrieve.3 &amp;&amp; echo 'manifying lonretrieve.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1318,12 +2416,16 @@ loncom/build/pod2man.sh ../publisher/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonretrieve.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonretrieve.html</target>
+<source>doc/lib/perl/Apache/lonretrieve.html</source>
+<target dist='default'>
+home/httpd/html/adm/help/lib/perl/Apache/lonretrieve.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonretrieve.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../publisher/lonretrieve.pm > ../../doc/api/Apache/lonretrieve.html && echo 'pod2html lonretrieve.pm'
+loncom/build/pod2html.sh ../publisher/lonretrieve.pm &gt; \
+../../doc/lib/perl/Apache/lonretrieve.html &amp;&amp; \
+echo 'pod2html lonretrieve.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1344,7 +2446,8 @@ Helper functions when in homework edit m
 <categoryname>doc</categoryname>
 <description>man page for edit.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../homework/edit.pm > ../../doc/man/Apache__edit.3 && echo 'manifying edit.pm'
+loncom/build/pod2man.sh ../homework/edit.pm &gt; ../../doc/man/Apache__edit.3 &amp;&amp; \
+echo 'manifying edit.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1352,12 +2455,15 @@ loncom/build/pod2man.sh ../homework/edit
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/edit.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/edit.html</target>
+<source>doc/lib/perl/Apache/edit.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/edit.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for edit.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../homework/edit.pm > ../../doc/api/Apache/edit.html && echo 'pod2html edit.pm'
+loncom/build/pod2html.sh ../homework/edit.pm &gt; \
+../../doc/lib/perl/Apache/edit.html \
+&amp;&amp; echo 'pod2html edit.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1419,11 +2525,51 @@ them roles.
 <status>works/unverified</status>
 </file>
 <file>
-<source>loncom/interface/lonchart.pm</source>
-<target dist='default'>home/httpd/lib/perl/Apache/lonchart.pm</target>
+<source>loncom/interface/lonhtmlcommon.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonhtmlcommon.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Produces simple LectureOnline-like student assessment performance chart
+Contains a set of functions that generate html controls and data layouts
+</description>
+</file>
+<file>
+<source>loncom/localize/lonlocal.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonlocal.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Contains the &mt access function to Locale::Maketext
+</description>
+</file>
+<file>
+<source>loncom/localize/localize.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/localize.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Localization class for Locale::Maketext
+</description>
+</file>
+<fileglob>
+<glob>*.pm</glob>
+<sourcedir>loncom/localize/localize/</sourcedir>
+<targetdir dist='default'>
+home/httpd/lib/perl/Apache/localize/</targetdir>
+<categoryname>static conf</categoryname>
+<description>
+Translation files.
+</description>
+<filenames>
+de.pm;
+pt.pm;
+ja.pm;
+tr.pm;
+</filenames>
+</fileglob>
+<file>
+<source>loncom/interface/loncoursedata.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/loncoursedata.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Common functions for handling student course data (download and process)
 </description>
 </file>
 <file>
@@ -1442,7 +2588,8 @@ user, domain, home_server, course_id.
 <categoryname>doc</categoryname>
 <description>man page for loncommon.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../interface/loncommon.pm > ../../doc/man/Apache__loncommon.3 && echo 'manifying loncommon.pm'
+loncom/build/pod2man.sh ../interface/loncommon.pm &gt; \
+../../doc/man/Apache__loncommon.3 &amp;&amp; echo 'manifying loncommon.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1450,12 +2597,15 @@ loncom/build/pod2man.sh ../interface/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/loncommon.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/loncommon.html</target>
+<source>doc/lib/perl/Apache/loncommon.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/loncommon.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for loncommon.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../interface/loncommon.pm > ../../doc/api/Apache/loncommon.html && echo 'pod2html loncommon.pm'
+loncom/build/pod2html.sh ../interface/loncommon.pm &gt; \
+../../doc/lib/perl/Apache/loncommon.html &amp;&amp; \
+echo 'pod2html loncommon.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1494,6 +2644,43 @@ assignment.
 </description>
 <status>works/unverified</status>
 </file>
+
+<file>
+  <source>loncom/homework/chemresponse.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/chemresponse.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+    Handle the tags organicresponse/structure and reationresponse
+  </description>
+  <status>works/unverified</status>
+</file>
+
+<fileglob>
+  <glob>*.*</glob>
+  <sourcedir>loncom/html/adm/jme/</sourcedir>
+  <targetdir dist='default'>home/httpd/html/adm/jme/</targetdir>
+  <categoryname>interface file</categoryname>
+  <description>
+    JME files, for editing organic structures
+  </description>
+  <filenames>
+JME.jar;
+jme.gif;
+jme_help.html;
+nitro.gif;
+smiles.gif
+  </filenames>
+</fileglob>
+
+<file>
+  <source>loncom/homework/convertjme.pl</source>
+  <target dist='default'>home/httpd/cgi-bin/convertjme.pl</target>
+  <categoryname>script</categoryname>
+  <description>
+    Dynamically converts JME strings into either a png or ps file.
+  </description>
+</file>
+
 <file>
 <source>loncom/interface/lontest.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lontest.pm</target>
@@ -1572,6 +2759,73 @@ Handles navigational maps.
 <status>works/unverified</status>
 </file>
 <file>
+<source>doc/man/Apache__lonnavmaps.3</source>
+<target dist='default'>usr/man/man3/Apache::lonnavmaps.3</target>
+<categoryname>doc</categoryname>
+<description>man page for lonnavmaps.pm</description>
+<build trigger='always run'>
+loncom/build/pod2man.sh ../../loncom/interface/lonnavmaps.pm &gt; \
+../../doc/man/Apache__lonnavmaps.3 &amp;&amp; echo 'manifying lonnavmaps.pm'
+</build>
+<status>works/unverified</status>
+<dependencies>
+../../loncom/interface/lonnavmaps.pm
+</dependencies>
+</file>
+<file>
+<source>doc/lib/perl/Apache/lonnavmaps.html</source>
+<target dist='default'>
+home/httpd/html/adm/help/lib/perl/Apache/lonnavmaps.html
+</target>
+<categoryname>doc</categoryname>
+<description>POD-derived page for lonnavmaps.pm</description>
+<build trigger='always run'>
+loncom/build/pod2html.sh ../../loncom/interface/lonnavmaps.pm &gt; \
+../../doc/lib/perl/Apache/lonnavmaps.html &amp;&amp; \
+echo 'pod2html lonnavmaps.pm'
+</build>
+<status>works/unverified</status>
+<dependencies>
+../../loncom/interface/lonnavmaps.pm
+</dependencies>
+</file>
+<file>
+<source>loncom/interface/lonhelper.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonhelper.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Helper framework.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/html/adm/helper/parameter.helper</source>
+<target dist='default'>home/httpd/html/adm/helper/parameter.helper</target>
+<categoryname>handler</categoryname>
+<description>
+Parameter setting helper.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/html/adm/helper/course.initialization.helper</source>
+<target dist='default'>home/httpd/html/adm/helper/course.initialization.helper</target>
+<categoryname>handler</categoryname>
+<description>
+Course initialization helper.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonquickgrades.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonquickgrades.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Student quick grades interface.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/lonpreferences.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonpreferences.pm</target>
 <categoryname>handler</categoryname>
@@ -1600,12 +2854,22 @@ Handles a searchable catalogue.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonmysql.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonmysql.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Provides utility functions for creating and accessing mysql database tables.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>doc/man/Apache__lonsearchcat.3</source>
 <target dist='default'>usr/man/man3/Apache::lonsearchcat.3</target>
 <categoryname>doc</categoryname>
 <description>man page for lonsearchcat.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../interface/lonsearchcat.pm > ../../doc/man/Apache__lonsearchcat.3 && echo 'manifying lonsearchcat.pm'
+loncom/build/pod2man.sh ../interface/lonsearchcat.pm &gt; \
+../../doc/man/Apache__lonsearchcat.3 &amp;&amp; echo 'manifying lonsearchcat.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1613,12 +2877,16 @@ loncom/build/pod2man.sh ../interface/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonsearchcat.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonsearchcat.html</target>
+<source>doc/lib/perl/Apache/lonsearchcat.html</source>
+<target dist='default'>
+home/httpd/html/adm/help/lib/perl/Apache/lonsearchcat.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonsearchcat.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../interface/lonsearchcat.pm > ../../doc/api/Apache/lonsearchcat.html && echo 'pod2html lonsearchcat.pm'
+loncom/build/pod2html.sh ../interface/lonsearchcat.pm &gt; \
+../../doc/lib/perl/Apache/lonsearchcat.html &amp;&amp; \
+echo 'pod2html lonsearchcat.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1626,6 +2894,15 @@ loncom/build/pod2html.sh ../interface/lo
 </dependencies>
 </file>
 <file>
+<source>loncom/interface/lonmanagekeys.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonmanagekeys.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Allows users with "mky" privileges to generate and manage course access keys.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/londropadd.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/londropadd.pm</target>
 <categoryname>handler</categoryname>
@@ -1662,13 +2939,49 @@ problems and assignments.
 <status>works/unverified</status>
 </file>
 <file>
-<source>loncom/interface/lonspreadsheet.pm</source>
+<source>loncom/interface/spreadsheet/lonspreadsheet.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonspreadsheet.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Spreadsheets are completely web-based.
-They exist on the level of a whole course, a student, and individual
-assessments.
+The top level interface for the display and editing of spreadsheets.  There
+are three levels of spreadsheet.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/spreadsheet/Spreadsheet.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/Spreadsheet.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Defines the parent object of each spreadsheet type (classcalc, studentcalc,
+assesscalc).
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/spreadsheet/classcalc.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/classcalc.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Defines the specifics of the course level spreadsheet.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/spreadsheet/studentcalc.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/studentcalc.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Defines the specifics of the student level spreadsheet.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/spreadsheet/assesscalc.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/assesscalc.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Defines the specifics of the assessment level spreadsheet.
 </description>
 <status>works/unverified</status>
 </file>
@@ -1687,7 +3000,8 @@ Handler to resolve ambiguous file locati
 <categoryname>doc</categoryname>
 <description>man page for lonparmset.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../interface/lonparmset.pm > ../../doc/man/Apache__lonparmset.3 && echo 'manifying lonparmset.pm'
+loncom/build/pod2man.sh ../interface/lonparmset.pm &gt; \
+../../doc/man/Apache__lonparmset.3 &amp;&amp; echo 'manifying lonparmset.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1695,12 +3009,15 @@ loncom/build/pod2man.sh ../interface/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonparmset.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonparmset.html</target>
+<source>doc/lib/perl/Apache/lonparmset.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonparmset.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonparmset.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../interface/lonparmset.pm > ../../doc/api/Apache/lonparmset.html && echo 'pod2html lonparmset.pm'
+loncom/build/pod2html.sh ../interface/lonparmset.pm &gt; \
+../../doc/lib/perl/Apache/lonparmset.html &amp;&amp; \
+echo 'pod2html lonparmset.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1732,7 +3049,8 @@ Publishes an LON-CAPA educational resour
 <categoryname>doc</categoryname>
 <description>man page for lonpublisher.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../publisher/lonpublisher.pm > ../../doc/man/Apache__lonpublisher.3 && echo 'manifying lonpublisher.pm'
+loncom/build/pod2man.sh ../publisher/lonpublisher.pm &gt; \
+../../doc/man/Apache__lonpublisher.3 &amp;&amp; echo 'manifying lonpublisher.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1740,12 +3058,16 @@ loncom/build/pod2man.sh ../publisher/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonpublisher.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonpublisher.html</target>
+<source>doc/lib/perl/Apache/lonpublisher.html</source>
+<target dist='default'>
+home/httpd/html/adm/help/lib/perl/Apache/lonpublisher.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonpublisher.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../publisher/lonpublisher.pm > ../../doc/api/Apache/lonpublisher.html && echo 'pod2html lonpublisher.pm'
+loncom/build/pod2html.sh ../publisher/lonpublisher.pm &gt; \
+../../doc/lib/perl/Apache/lonpublisher.html &amp;&amp; \
+echo 'pod2html lonpublisher.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1762,6 +3084,15 @@ Has routines which control the remote co
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonremote.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonremote.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to lauch and collapse the remote control.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>rat/lonpageflip.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonpageflip.pm</target>
 <categoryname>handler</categoryname>
@@ -1787,6 +3118,15 @@ Homework remote control.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/html/res/adm/pages/chatroom.html</source>
+<target dist='default'>home/httpd/html/res/adm/pages/chatroom.html</target>
+<categoryname>handler</categoryname>
+<description>
+Establishes frameset for chatroom
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/html/res/adm/pages/annotator/admannotations.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/admannotations.pm</target>
 <categoryname>handler</categoryname>
@@ -1831,7 +3171,8 @@ bundles pages into one page
 <categoryname>doc</categoryname>
 <description>man page for lonpage.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../../rat/lonpage.pm > ../../doc/man/Apache__lonpage.3 && echo 'manifying lonpage.pm'
+loncom/build/pod2man.sh ../../rat/lonpage.pm &gt; \
+../../doc/man/Apache__lonpage.3 &amp;&amp; echo 'manifying lonpage.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1839,12 +3180,14 @@ loncom/build/pod2man.sh ../../rat/lonpag
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonpage.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonpage.html</target>
+<source>doc/lib/perl/Apache/lonpage.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonpage.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonnet.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../../rat/lonpage.pm > ../../doc/api/Apache/lonpage.html && echo 'pod2html lonpage.pm'
+loncom/build/pod2html.sh ../../rat/lonpage.pm &gt; \
+../../doc/lib/perl/Apache/lonpage.html &amp;&amp; echo 'pod2html lonpage.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1856,7 +3199,7 @@ loncom/build/pod2html.sh ../../rat/lonpa
 <target dist='default'>home/httpd/lib/perl/Apache/lonuserstate.pm</target>
 <categoryname>handler</categoryname>
 <description>
-compile course into binary data structure (in loncom/rat)
+compile course into binary data structure
 </description>
 <status>works/unverified</status>
 </file>
@@ -1866,7 +3209,8 @@ compile course into binary data structur
 <categoryname>doc</categoryname>
 <description>man page for lonnet.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../../rat/lonuserstate.pm > ../../doc/man/Apache__lonuserstate.3 && echo 'manifying lonuserstate.pm'
+loncom/build/pod2man.sh ../../rat/lonuserstate.pm &gt; \
+../../doc/man/Apache__lonuserstate.3 &amp;&amp; echo 'manifying lonuserstate.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1874,12 +3218,16 @@ loncom/build/pod2man.sh ../../rat/lonuse
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonuserstate.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonuserstate.html</target>
+<source>doc/lib/perl/Apache/lonuserstate.html</source>
+<target dist='default'>
+home/httpd/html/adm/help/lib/perl/Apache/lonuserstate.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonuserstate.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../../rat/lonuserstate.pm > ../../doc/api/Apache/lonuserstate.html && echo 'pod2html lonuserstate.pm'
+loncom/build/pod2html.sh ../../rat/lonuserstate.pm &gt; \
+../../doc/lib/perl/Apache/lonuserstate.html &amp;&amp; \
+echo 'pod2html lonuserstate.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -1891,7 +3239,7 @@ loncom/build/pod2html.sh ../../rat/lonus
 <target dist='default'>home/httpd/lib/perl/Apache/lontex.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Handler for tex files (somewhere in modules)
+Handler for tex files
 </description>
 <status>works/unverified</status>
 </file>
@@ -1960,6 +3308,39 @@ implements &lt;script&gt;, &lt;scriptlib
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/xml/languagetags.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/languagetags.pm</target>
+<categoryname>handler</categoryname>
+<description>
+implements &lt;mt&gt;
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/homework/randomlylabel.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/randomlylabel.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for compositing images, and text together.
+</description>
+</file>
+<file>
+<source>loncom/homework/rankresponse.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/rankresponse.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for rankresponse
+</description>
+</file>
+<file>
+<source>loncom/homework/matchresponse.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/matchresponse.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for matchresponse
+</description>
+</file>
+<file>
 <source>loncom/homework/randomlabel.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/randomlabel.pm</target>
 <categoryname>handler</categoryname>
@@ -2016,15 +3397,37 @@ handles request to the CAPA homework pro
 <status>works/unverified</status>
 </file>
 <file>
-<source>loncom/auth/localauth.pm</source>
-<target dist='default'>home/httpd/lib/perl/localauth.pm</target>
+<source>loncom/xml/Safe.pm</source>
+<target dist='default'>home/httpd/lib/perl/Safe.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Local authentication mechanism (meant to be customized).
+Meant to safely substitute for CPAN version of Safe.
+Allows for safely executing embedded perl comands in
+a way that does not threaten the operating system.
 </description>
 <status>works/unverified</status>
 </file>
 <file>
+  <source>loncom/auth/localauth.pm</source>
+  <target dist='default'>home/httpd/lib/perl/localauth-std.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+Local authentication mechanism.  The target file is meant as a template
+for a localauth.pm file.  The target file with the -std suffix is not
+used directly by any software program; it is just a template file.
+  </description>
+  <status>works/unverified</status>
+</file>
+<file>
+  <source>loncom/auth/localauth.pm</source>
+  <target dist='default'>home/httpd/lib/perl/localauth.pm</target>
+  <categoryname>conf</categoryname>
+  <description>
+Local authentication mechanism.  
+  </description>
+  <status>works/unverified</status>
+</file>
+<file>
 <source>loncom/auth/lonacc.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonacc.pm</target>
 <categoryname>handler</categoryname>
@@ -2042,7 +3445,8 @@ as coordinating access to educational re
 <categoryname>doc</categoryname>
 <description>man page for lonacc.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../auth/lonacc.pm > ../../doc/man/Apache__lonacc.3 && echo 'manifying lonacc.pm'
+loncom/build/pod2man.sh ../auth/lonacc.pm &gt; \
+../../doc/man/Apache__lonacc.3 &amp;&amp; echo 'manifying lonacc.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2050,12 +3454,14 @@ loncom/build/pod2man.sh ../auth/lonacc.p
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonacc.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonacc.html</target>
+<source>doc/lib/perl/Apache/lonacc.html</source>
+<target dist='default'>
+home/httpd/html/adm/help/lib/perl/Apache/lonacc.html</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonacc.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../auth/lonacc.pm > ../../doc/api/Apache/lonacc.html && echo 'pod2html lonacc.pm'
+loncom/build/pod2html.sh ../auth/lonacc.pm &gt; \
+../../doc/lib/perl/Apache/lonacc.html &amp;&amp; echo 'pod2html lonacc.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2072,12 +3478,41 @@ access handler for file transfers
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/auth/lontokacc.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lontokacc.pm</target>
+<categoryname>handler</categoryname>
+<description>
+handler for inter-server transfer of token accessed files, includes
+cleanup handler to remove file when successfully done
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/auth/lonuploadedacc.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonuploadedacc.pm</target>
+<categoryname>handler</categoryname>
+<description>
+access handler for user uploaded files
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/lontrans.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lontrans.pm</target>
+<categoryname>handler</categoryname>
+<description>
+URI to filename translation
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>doc/man/Apache__lonracc.3</source>
 <target dist='default'>usr/man/man3/Apache::lonracc.3</target>
 <categoryname>doc</categoryname>
 <description>man page for lonracc.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../auth/lonracc.pm > ../../doc/man/Apache__lonracc.3 && echo 'manifying lonracc.pm'
+loncom/build/pod2man.sh ../auth/lonracc.pm &gt; \
+../../doc/man/Apache__lonracc.3 &amp;&amp; echo 'manifying lonracc.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2085,12 +3520,14 @@ loncom/build/pod2man.sh ../auth/lonracc.
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonracc.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonracc.html</target>
+<source>doc/lib/perl/Apache/lonracc.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonracc.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonracc.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../auth/lonracc.pm > ../../doc/api/Apache/lonracc.html && echo 'pod2html lonracc.pm'
+loncom/build/pod2html.sh ../auth/lonracc.pm &gt; \
+../../doc/lib/perl/Apache/lonracc.html &amp;&amp; echo 'pod2html lonracc.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2121,7 +3558,8 @@ for the "priv"-type access, the resource
 <categoryname>doc</categoryname>
 <description>man page for loncacc.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../auth/loncacc.pm > ../../doc/man/Apache__loncacc.3 && echo 'manifying loncacc.pm'
+loncom/build/pod2man.sh ../auth/loncacc.pm &gt; ../../doc/man/Apache__loncacc.3 \
+&amp;&amp; echo 'manifying loncacc.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2129,12 +3567,14 @@ loncom/build/pod2man.sh ../auth/loncacc.
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/loncacc.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/loncacc.html</target>
+<source>doc/lib/perl/Apache/loncacc.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/loncacc.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for loncacc.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../auth/loncacc.pm > ../../doc/api/Apache/loncacc.html && echo 'pod2html loncacc.pm'
+loncom/build/pod2html.sh ../auth/loncacc.pm &gt; \
+../../doc/lib/perl/Apache/loncacc.html &amp;&amp; echo 'pod2html loncacc.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2188,7 +3628,8 @@ class.
 <categoryname>doc</categoryname>
 <description>man page for lonroles.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../auth/lonroles.pm > ../../doc/man/Apache__lonroles.3 && echo 'manifying lonroles.pm'
+loncom/build/pod2man.sh ../auth/lonroles.pm &gt; \
+../../doc/man/Apache__lonroles.3 &amp;&amp; echo 'manifying lonroles.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2196,12 +3637,14 @@ loncom/build/pod2man.sh ../auth/lonroles
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonroles.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonroles.html</target>
+<source>doc/lib/perl/Apache/lonroles.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonroles.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonroles.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../auth/lonroles.pm > ../../doc/api/Apache/lonroles.html && echo 'pod2html lonroles.pm'
+loncom/build/pod2html.sh ../auth/lonroles.pm &gt; \
+../../doc/lib/perl/Apache/lonroles.html &amp;&amp; echo 'pod2html lonroles.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2223,7 +3666,8 @@ cross server filesystem browser
 <categoryname>doc</categoryname>
 <description>man page for lonindexer.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../interface/lonindexer.pm > ../../doc/man/Apache__lonindexer.3 && echo 'manifying lonindexer.pm'
+loncom/build/pod2man.sh ../interface/lonindexer.pm &gt; \
+../../doc/man/Apache__lonindexer.3 &amp;&amp; echo 'manifying lonindexer.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2231,12 +3675,15 @@ loncom/build/pod2man.sh ../interface/lon
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonindexer.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonindexer.html</target>
+<source>doc/lib/perl/Apache/lonindexer.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonindexer.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonindexer.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../interface/lonindexer.pm > ../../doc/api/Apache/lonindexer.html && echo 'pod2html lonindexer.pm'
+loncom/build/pod2html.sh ../interface/lonindexer.pm &gt; \
+../../doc/lib/perl/Apache/lonindexer.html &amp;&amp; \
+echo 'pod2html lonindexer.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2277,7 +3724,8 @@ symbols to and from more descriptive phr
 <categoryname>doc</categoryname>
 <description>man page for lonnet.pm</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh ../lonnet/perl/lonnet.pm > ../../doc/man/Apache__lonnet.3 && echo 'manifying lonnet.pm'
+loncom/build/pod2man.sh ../lonnet/perl/lonnet.pm &gt; \
+../../doc/man/Apache__lonnet.3 &amp;&amp; echo 'manifying lonnet.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2285,12 +3733,14 @@ loncom/build/pod2man.sh ../lonnet/perl/l
 </dependencies>
 </file>
 <file>
-<source>doc/api/Apache/lonnet.html</source>
-<target dist='default'>home/httpd/html/adm/help/api/Apache/lonnet.html</target>
+<source>doc/lib/perl/Apache/lonnet.html</source>
+<target dist='default'>home/httpd/html/adm/help/lib/perl/Apache/lonnet.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for lonnet.pm</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh ../lonnet/perl/lonnet.pm > ../../doc/api/Apache/lonnet.html && echo 'pod2html lonnet.pm'
+loncom/build/pod2html.sh ../lonnet/perl/lonnet.pm &gt; \
+../../doc/lib/perl/Apache/lonnet.html &amp;&amp; echo 'pod2html lonnet.pm'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -2303,6 +3753,18 @@ loncom/build/pod2html.sh ../lonnet/perl/
 <categoryname>interface file</categoryname>
 <description>bumps to login</description>
 </file>
+<file>
+<source>loncom/html/index.html</source>
+<target dist='default'>home/httpd/html/origindex.html</target>
+<categoryname>interface file</categoryname>
+<description>bumps to login, backup for takeonline</description>
+</file>
+<file>
+<source>loncom/html/favicon.ico</source>
+<target dist='default'>home/httpd/html/favicon.ico</target>
+<categoryname>interface file</categoryname>
+<description>Bookmark and tab icon</description>
+</file>
 <link>
 <linkto>etc/mime.types</linkto>
 <target dist='default'>etc/httpd/conf/mime.types</target>
@@ -2366,6 +3828,22 @@ javascript
 </description>
 </file>
 <file>
+<source>rat/client/extpickcode.html</source>
+<target dist='default'>home/httpd/html/adm/rat/extpickcode.html</target>
+<categoryname>interface file</categoryname>
+<description>
+javascript
+</description>
+</file>
+<file>
+<source>rat/client/extpickframe.html</source>
+<target dist='default'>home/httpd/html/adm/rat/extpickframe.html</target>
+<categoryname>interface file</categoryname>
+<description>
+javascript
+</description>
+</file>
+<file>
 <source>rat/client/map.html</source>
 <target dist='default'>home/httpd/html/adm/rat/map.html</target>
 <categoryname>interface file</categoryname>
@@ -2381,6 +3859,14 @@ bumper
 A blank page with very minimal HTML structural elements.
 </description>
 </file>
+<file>
+<source>rat/client/loading.html</source>
+<target dist='default'>home/httpd/html/adm/rat/loading.html</target>
+<categoryname>interface file</categoryname>
+<description>
+A blank page which calls drawwindow in its opener after being loaded.
+</description>
+</file>
 <fileglob>
 <glob>*.gif</glob>
 <sourcedir>rat/images/</sourcedir>
@@ -2524,52 +4010,94 @@ lonlogo_broken.mov
 <targetdir dist='default'>home/httpd/html/adm/lonIcons/</targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-logos
+logos and general widget icons
 </description>
 <filenames>
 SMETE_white.gif;
+aboutlon.gif;
+aboutlon_pt.gif;
+aboutlon_de.gif;
+accessbutton.gif;
+accessbutton_pt.gif;
+accessbutton_de.gif;
+angry.gif;
 arrow_up.gif;
+bigsmile.gif;
+branch.gif;
 cab.gif;
 cab_big.gif;
 capapanel.gif;
+check.gif;
 class.gif;
 class_big.gif;
+coolindiff.gif;
+coolsmile.gif;
+cry.gif;
 dvi.gif;
 dvi_big.gif;
 eps.gif;
 eps_big.gif;
 exam.gif;
 exam_big.gif;
+fillbottom.gif;
+fillleft.gif;
+fillright.gif;
+filltop.gif;
 folder_closed.gif;
 folder_opened.gif;
 folder_pointer_closed.gif;
 folder_pointer_opened.gif;
 form.gif;
 form_big.gif;
+frowny.gif;
 gif.gif;
 gif_big.gif;
+header.gif;
+hrrm.gif;
 htm.gif;
 html.gif;
 html_big.gif;
+huh.gif;
 jar.gif;
 jar_big.gif;
 jpg.gif;
 jpg_big.gif;
 latex.gif;
+library.gif;
+lipsrsealed.gif;
+lite.gif;
 liteani.gif;
+litetext.gif;
 lolpanel.gif;
 lonanim.gif;
 lonanimend.gif;
+loncapalogo.gif;
 lonhelplogos.gif;
 lonhelptop.gif;
 lonlogo.gif;
 lonlogos.gif;
+lowerleft.gif;
+lowerright.gif;
+minilogo.gif;
 meta.gif;
 meta_big.gif;
 mov.gif;
 mov_big.gif;
 move_up.gif;
 move_down.gif;
+navmap.correct.gif;
+navmap.ellipsis.gif;
+navmap.open.gif;
+navmap.page.open.gif;
+navmap.page.closed.gif;
+navmap.page.open.nomanip.gif;
+navmap.page.closed.nomanip.gif;
+navmap.wrong.gif;
+navmap.folder.open.gif;
+navmap.folder.closed.gif;
+navmap.folder.open.nomanip.gif;
+navmap.folder.closed.nomanip.gif;
+neutral.gif;
 page.gif;
 page_big.gif;
 pdf.gif;
@@ -2580,6 +4108,7 @@ problem.gif;
 problem_big.gif;
 ps.gif;
 ps_big.gif;
+rolleyes.gif;
 quill.gif;
 quiz.gif;
 quiz_big.gif;
@@ -2588,6 +4117,8 @@ sequence.gif;
 sequence_big.gif;
 server.gif;
 server_big.gif;
+shocked.gif;
+smiley.gif;
 srvbad.gif;
 srvempty.gif;
 srvgood.gif;
@@ -2597,12 +4128,18 @@ survey.gif;
 survey_big.gif;
 tex.gif;
 tex_big.gif;
+tth.gif;
 txt.gif;
 txt_big.gif;
 unknown.gif;
 unknown_big.gif;
+upperleft.gif;
+upperright.gif;
 user.gif;
 user_big.gif;
+userauthentication.gif;
+userauthentication_pt.gif;
+userauthentication_de.gif;
 wav.gif;
 wav_big.gif;
 white_space_20_22.gif;
@@ -2616,6 +4153,7 @@ whitespace6.gif;
 whitespace7.gif;
 whitespace8.gif;
 whitespace9.gif;
+wink.gif;
 xml.gif;
 xml_big.gif;
 zip.gif;
@@ -2628,15 +4166,14 @@ zip_big.gif
 <targetdir dist='default'>home/httpd/html/adm/lonMisc/</targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-Miscellaneous resources.  Respectively: button for catalog,
-button to set parameters in a page,
-button to do regrades, button to check on problem submissions,
+Miscellaneous resources.
 </description>
 <filenames>
 authorfeed.gif;
 bomb.gif;
 cat_button.gif;
 chat.gif;
+eval_button.gif;
 feedback.gif;
 pprm_button.gif;
 pgrd_button.gif;
@@ -2644,9 +4181,9 @@ subm_button.gif
 </filenames>
 </fileglob>
 <file>
-<source>loncom/xml/tth.pm</source>
-<target dist='default'>usr/lib/perl5/site_perl/5.005/tth.pm</target>
-<target dist='redhat7.1'>usr/lib/perl5/site_perl/5.6.0/tth.pm</target>
+<source>modules/TexConvert/tthperl/tth.pm</source>
+<target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/tth.pm</target>
+<target dist='default'>home/httpd/lib/perl/tth.pm</target>
 <categoryname>system file</categoryname>
 <description>
 perl module for invoking functions specific to TeX-to-HTML conversion
@@ -2660,9 +4197,86 @@ and in this way is treated as though it
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/xml/LCParser.pm</source>
+<target dist='default'>home/httpd/lib/perl/HTML/LCParser.pm</target>
+<categoryname>system file</categoryname>
+<description>
+perl module for parsing HTML in a way that really works and is thoroughly
+tested
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+  <source>loncom/LondConnection.pm</source>
+  <target dist='default'>home/httpd/lib/perl/LONCAPA/LondConnection.pm</target>
+  <categoryname>system file</categoryname>
+  <description>
+     Manages a connection between a lonc proxy daemon and the lond server
+     in the remote node.
+  </description>
+  <status>works/verified</status>
+</file>
+<file>
+  <source>loncom/LondTransaction.pm</source>
+  <target dist='default'>home/httpd/lib/perl/LONCAPA/LondTransaction.pm</target>
+  <categoryname>system file</categoryname>
+  <description>
+	Handles a single lon-capa insternal transaction
+  </description>
+  <status>works/verified</status>
+</file>
+<file>
+   <source>loncom/types/HashIterator.pm</source>
+   <target dist='default'>home/httpd/lib/perl/LONCAPA/HashIterator.pm</target>
+   <categoryname>system file</categoryname>
+   <description>
+      Provides support to iterate through opaque hashes hidden e.g. within 
+      object private data.
+   </description>
+   <status>works/verified</status>
+</file>
+<file>
+   <source>loncom/types/Queue.pm</source>
+   <target dist='default'>home/httpd/lib/perl/LONCAPA/Queue.pm</target>
+   <categoryname>system file</categoryname>
+   <description>
+     Provides a FIFO queue class.
+   </description>
+   <status>works/verified</status>
+</file>
+<file>
+   <source>loncom/types/Stack.pm</source>
+   <target dist='default'>home/httpd/lib/perl/LONCAPA/Stack.pm</target>
+   <categoryname>system file</categoryname>
+   <description>
+     Provides a LIFO stack class.
+   </description>
+   <status>works/verified</status>
+</file>
+<file>
+   <source>loncom/loncnew</source>
+   <target dist='default'>home/httpd/perl/loncnew</target>
+   <categoryname>script</categoryname>
+   <description>
+	  Proxy server for remote loncapa requests.
+          Needs CPAN Event module.
+   </description>
+</file>
+<file>
+<source>loncom/configuration/Configuration.pm</source>
+<target dist='default'>home/httpd/lib/perl/LONCAPA/Configuration.pm</target>
+<categoryname>system file</categoryname>
+<description>
+Configuration file reader (looks in /etc/httpd/conf/); accepts
+a list of *.conf files to inspect for PerlSetVar key/value
+entries.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>modules/TexConvert/tthperl/tth.so</source>
-<target dist='default'>usr/lib/perl5/site_perl/5.005/tth.so</target>
-<target dist='redhat7.1'>usr/lib/perl5/site_perl/5.6.0/tth.so</target>
+<target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/tth.so</target>
+<target dist='default'>home/httpd/lib/perl/tth.so</target>
 <categoryname>system file</categoryname>
 <description>
 shared library file for dynamic loading and unloading
@@ -2677,15 +4291,15 @@ related to this file during the build pr
 modules/TexConvert/tthperl/commands
 </build>
 <status>works/unverified</status>
-<dependencies>
+<privatedependencies>
 ../tthdynamic/tthfunc.c;
 ../ttmdynamic/ttmfunc.c
-</dependencies>
+</privatedependencies>
 </file>
 <file>
 <source>loncom/homework/caparesponse/capa.pm</source>
-<target dist='default'>usr/lib/perl5/site_perl/5.005/capa.pm</target>
-<target dist='redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.pm</target>
+<target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.pm</target>
+<target dist='default'>home/httpd/lib/perl/capa.pm</target>
 <categoryname>system file</categoryname>
 <description>
 perl module for invoking functions specific to CAPA
@@ -2699,8 +4313,8 @@ the build process however.
 </file>
 <file>
 <source>loncom/homework/caparesponse/capa.bs</source>
-<target dist='default'>usr/lib/perl5/site_perl/5.005/capa.bs</target>
-<target dist='redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.bs</target>
+<target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.bs</target>
+<target dist='default'>home/httpd/lib/perl/capa.bs</target>
 <categoryname>system file</categoryname>
 <description>
 bootstrap file associated with dynamic loading of this module on multiple
@@ -2715,8 +4329,8 @@ the build process however.
 </file>
 <file>
 <source>loncom/homework/caparesponse/capa.so</source>
-<target dist='default'>usr/lib/perl5/site_perl/5.005/capa.so</target>
-<target dist='redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.so</target>
+<target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.so</target>
+<target dist='default'>home/httpd/lib/perl/capa.so</target>
 <categoryname>system file</categoryname>
 <description>
 shared library file for dynamic loading and unloading
@@ -2726,7 +4340,34 @@ loncom/homework/caparesponse/commands
 </build>
 <dependencies>
 caparesponse.c;
-caparesponse.pm
+caparesponse.pm;
+README;
+Makefile.PL;
+capa.i;
+commands;
+../../../CAPA/pProj/Makefile;
+../../../CAPA/pProj/capaGrammarDef.y;
+../../../CAPA/pProj/capaFormula.y;
+../../../CAPA/pProj/capaLexerDef.flex;
+../../../CAPA/pProj/capaFunction.c;
+../../../CAPA/pProj/capaParserUtils.c;
+../../../CAPA/pProj/capaMapExpr.c;
+../../../CAPA/pProj/capaUnit.c;
+../../../CAPA/pProj/com.c;
+../../../CAPA/pProj/linpack.c;
+../../../CAPA/pProj/ranlib.c;
+../../../CAPA/pProj/capaCgiUtils.c;
+../../../CAPA/pProj/capaSubjective.c;
+../../../CAPA/pProj/capaRQO.c;
+../../../CAPA/pProj/capaFormulaLexer.c;
+../../../CAPA/pProj/capaCommon.c;
+../../../CAPA/pProj/capaCommon.h;
+../../../CAPA/pProj/ranlib.h;
+../../../CAPA/pProj/capaCGI.h;
+../../../CAPA/pProj/capaFunction.h;
+../../../CAPA/pProj/capaRQO.h;
+../../../CAPA/pProj/capaParser.h;
+../../../CAPA/pProj/lex_debug.h
 </dependencies>
 </file>
 <fileglob>
@@ -2796,8 +4437,8 @@ javascript.
 </target>
 <categoryname>handler</categoryname>
 <description>
-Intended for providing perl functions for the <script></script> environment
-in a problem that was converted from lectureonline.
+Intended for providing perl functions for the &lt;script&gt;&lt;/script&gt;
+environment in a problem that was converted from lectureonline.
 </description>
 </file>
 <file>
@@ -2819,19 +4460,166 @@ Define unit prefixing and conversion for
 </description>
 </file>
 <fileglob>
+<glob>*.jpg</glob>
+<sourcedir>loncom/html/adm/lonInterFace/</sourcedir>
+<targetdir dist='default'>home/httpd/html/adm/lonInterFace/</targetdir>
+<categoryname>graphic file</categoryname>
+<description>Pages headers</description>
+<filenames>
+admin.jpg;
+author.jpg;
+coordinator.jpg;
+header.jpg;
+student.jpg;
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.jpg</glob>
+<sourcedir>loncom/html/adm/lonDomLogos/</sourcedir>
+<targetdir dist='default'>home/httpd/html/adm/lonDomLogos/</targetdir>
+<categoryname>graphic file</categoryname>
+<description>Logos of LON-CAPA domains (jpg)</description>
+<filenames>
+headermsu.jpg;
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.gif</glob>
+<sourcedir>loncom/html/adm/lonDomLogos/</sourcedir>
+<targetdir dist='default'>home/httpd/html/adm/lonDomLogos/</targetdir>
+<categoryname>graphic file</categoryname>
+<description>Logos of LON-CAPA domains (gif)</description>
+<filenames>
+103.gif;
+gerd.gif;
+mio.gif;
+msuvu.gif;
+ohiou.gif;
+rhs.gif;
+sfu.gif;
+tmcc.gif;
+umich.gif;
+worf.gif;
+annarbor.gif;
+elps.gif;
+gwu.gif;
+msudemo.gif;
+ndsu.gif;
+physnet.gif;
+sc.gif;
+Selwyn.gif;
+ucf.gif;
+unihalle.gif;
+wscc.gif;
+cps.gif;
+fsu.gif;
+lsd.gif;
+msu.gif;
+nsdl.gif;
+pmm.gif;
+sunysb.gif;
+udel.gif;
+uz.gif;
+fvl.gif;
+csm.gif;
+fit.gif;
+nau.gif;
+cmich.gif;
+UNICAMP.gif;
+glps.gif;
+BCHS.gif;
+headersfu.gif;
+uwsp.gif
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.tab</glob>
+<sourcedir>loncom/html/adm/lonDomColors/</sourcedir>
+<targetdir dist='default'>home/httpd/lonTabs/lonDomColors/</targetdir>
+<categoryname>conf</categoryname>
+<description>Designs of LON-CAPA domains</description>
+<filenames>
+annarbor.tab;
+default.tab;
+msu.tab;
+csm.tab;
+fit.tab;
+nau.tab;
+cmich.tab;
+UNICAMP.tab;
+fsu.tab;
+sfu.tab;
+worf.tab
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.gif</glob>
+<sourcedir>loncom/html/adm/lonLCDfont/</sourcedir>
+<targetdir dist='default'>home/httpd/html/adm/lonLCDfont/</targetdir>
+<categoryname>graphic file</categoryname>
+<description>LON-CAPA remote control LCD font</description>
+<filenames>
+0.gif;
+1.gif;
+2.gif;
+3.gif;
+4.gif;
+5.gif;
+6.gif;
+7.gif;
+8.gif;
+9.gif;
+a.gif;
+b.gif;
+c.gif;
+d.gif;
+e.gif;
+f.gif;
+g.gif;
+h.gif;
+i.gif;
+j.gif;
+k.gif;
+l.gif;
+m.gif;
+n.gif;
+o.gif;
+p.gif;
+q.gif;
+r.gif;
+s.gif;
+t.gif;
+u.gif;
+v.gif;
+w.gif;
+x.gif;
+y.gif;
+z.gif;
+ö.gif;
+ä.gif;
+ü.gif;
+ä.gif;
+ö.gif;
+ü.gif;
+colon.gif;
+hyphen.gif;
+slash.gif;
+space.gif;
+</filenames>
+</fileglob>
+<fileglob>
 <glob>*.gif</glob>
 <sourcedir>loncom/html/res/adm/pages/</sourcedir>
-<targetdir>home/httpd/html/res/adm/pages/</targetdir>
+<targetdir dist='default'>home/httpd/html/res/adm/pages/</targetdir>
 <categoryname>graphic file</categoryname>
 <description>icons used for the entire LON-CAPA user interface</description>
 <filenames>
-a.gif;
+anno.gif;
 anot.gif;
-b.gif;
 back.gif;
+bchat.gif;
 bkm.gif;
 brws.gif;
-c.gif;
 catalog.gif;
 ccrs.gif;
 chat.gif;
@@ -2840,71 +4628,49 @@ com.gif;
 courses.gif;
 cprv.gif;
 cstr.gif;
-d.gif;
 dempty.gif;
-e.gif;
+docs.gif;
 egrd.gif;
 empty.gif;
 enrl.gif;
 eval.gif;
-f.gif;
 fdbk.gif;
 feedback.gif;
 forw.gif;
-g.gif;
 grds.gif;
 group.gif;
-h.gif;
 help.gif;
-hyphen.gif;
-i.gif;
 info.gif;
-j.gif;
-k.gif;
-l.gif;
+keys.gif;
 ledblink.gif;
 ledgreen.gif;
 ledoff.gif;
 ledon.gif;
 ledsend.gif;
 logout.gif;
-m.gif;
 mrk.gif;
-n.gif;
 nav.gif;
 next.gif;
-o.gif;
-p.gif;
+nothumb.gif;
 parm.gif;
 pgrd.gif;
 pparm.gif;
 pref.gif;
 prev.gif;
 prt.gif;
-q.gif;
 qempty.gif;
-r.gif;
 reload.gif;
 remotebg.gif;
 res.gif;
 roles.gif;
-s.gif;
 sbkm.gif;
-space.gif;
 spacer.gif;
 sprs.gif;
 src.gif;
 stat.gif;
 subm.gif;
-t.gif;
 title.gif;
-u.gif;
-v.gif;
 vbkm.gif;
-w.gif;
-x.gif;
-y.gif;
-z.gif
 </filenames>
 </fileglob>
 <file>
@@ -2934,10 +4700,11 @@ renders the HTML (including image maps)
 <fileglob>
 <glob>*.gif</glob>
 <sourcedir>loncom/html/res/adm/pages/indexericons/</sourcedir>
-<targetdir>home/httpd/html/res/adm/pages/indexericons/</targetdir>
+<targetdir dist='default'>home/httpd/html/res/adm/pages/indexericons/
+</targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-icons used for the bookmark portion of the LON-CAPA user interface
+icons used for directory indexing and login screen
 </description>
 <filenames>
 a.gif;
@@ -3034,10 +4801,11 @@ world2.gif
 <fileglob>
 <glob>*.gif</glob>
 <sourcedir>loncom/html/res/adm/pages/bookmarkmenu/</sourcedir>
-<targetdir>home/httpd/html/res/adm/pages/bookmarkmenu/</targetdir>
+<targetdir dist='default'>home/httpd/html/res/adm/pages/bookmarkmenu/
+</targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-icons used for directory indexing and login screen
+icons used for the bookmark portion of the LON-CAPA user interface
 </description>
 <filenames>
 folder_anim.gif;
@@ -3068,10 +4836,11 @@ ur_corner.gif
 <fileglob>
 <glob>*.html</glob>
 <sourcedir>loncom/html/res/adm/pages/bookmarkmenu/</sourcedir>
-<targetdir>home/httpd/html/res/adm/pages/bookmarkmenu/</targetdir>
+<targetdir dist='default'>home/httpd/html/res/adm/pages/bookmarkmenu/
+</targetdir>
 <categoryname>interface file</categoryname>
 <description>
-associated with the frameset scheme of displaying bookmarks
+associated with the scheme of displaying bookmarks
 </description>
 <filenames>
 bookmarkmenu_toolbar.html;
@@ -3079,6 +4848,22 @@ blank.html;
 closechildren.html
 </filenames>
 </fileglob>
+<fileglob>
+<glob>*.*</glob>
+<sourcedir>loncom/html/res/adm/pages/reactionresponse/</sourcedir>
+<targetdir dist='default'>home/httpd/html/res/adm/pages/reactionresponse/</targetdir>
+<categoryname>interface file</categoryname>
+<description>
+Associated file for answering reactionresponse style questions
+</description>
+<filenames>
+reaction_editor.html;
+reaction_frame.html;
+reaction_help.html;
+reaction_viewer.html;
+reaction_window.html
+</filenames>
+</fileglob>
 <file>
 <source>loncom/html/res/adm/pages/bookmarkmenu/bookmarklib.js</source>
 <target dist='default'>
@@ -3089,9 +4874,18 @@ javascript for handling client-side inte
 </description>
 </file>
 <file>
+<source>loncom/build/CHECKRPMS</source>
+<target dist='default'>usr/local/loncapa/bin/CHECKRPMS</target>
+<categoryname>system script</categoryname>
+<description>
+manilla wrapper around check-rpms
+</description>
+<status>tested/documented/beta</status>
+</file>
+<file>
 <source>loncom/build/check-rpms</source>
-<target dist='default'>usr/local/bin/check-rpms</target>
-<categoryname>root script</categoryname>
+<target dist='default'>usr/local/loncapa/bin/check-rpms</target>
+<categoryname>system script</categoryname>
 <description>
 compare installed rpms with up-to-date distribution
 </description>
@@ -3103,7 +4897,8 @@ compare installed rpms with up-to-date d
 <categoryname>doc</categoryname>
 <description>man page for check-rpms</description>
 <build trigger='always run'>
-loncom/build/pod2man.sh check-rpms > ../../doc/man/check-rpms.1 && echo 'manifying check-rpms'
+loncom/build/pod2man.sh check-rpms &gt; ../../doc/man/check-rpms.1 &amp;&amp; \
+echo 'manifying check-rpms'
 </build>
 <status>beta</status>
 <dependencies>
@@ -3112,11 +4907,13 @@ loncom/build/pod2man.sh check-rpms > ../
 </file>
 <file>
 <source>doc/scripts/check-rpms.html</source>
-<target dist='default'>home/httpd/html/adm/help/scripts/check-rpms.html</target>
+<target dist='default'>home/httpd/html/adm/help/scripts/check-rpms.html
+</target>
 <categoryname>doc</categoryname>
 <description>POD-derived page for check-rpms</description>
 <build trigger='always run'>
-loncom/build/pod2html.sh check-rpms > ../../doc/scripts/check-rpms.html && echo 'pod2html checkrpms'
+loncom/build/pod2html.sh check-rpms &gt; ../../doc/scripts/check-rpms.html \
+&amp;&amp; echo 'pod2html checkrpms'
 </build>
 <status>works/unverified</status>
 <dependencies>
@@ -3125,12 +4922,14 @@ loncom/build/pod2html.sh check-rpms > ..
 </file>
 <file>
 <source>loncom/build/loncaparestoreconfigurations</source>
-<target dist='default'>usr/sbin/loncaparestoreconfigurations</target>
+<target dist='default'>usr/local/loncapa/sbin/loncaparestoreconfigurations
+</target>
 <categoryname>script</categoryname>
 <description>
-restores .rpmsave files after a LON-CAPA-base upgrade
+Updates .lpmlnew files with previous settings.  Also supports alternative
+schemes of settings-updating and file-overwriting.
 </description>
-<status>deprecated</status>
+<status>works/unverified</status>
 </file>
 <file>
 <source>loncom/cron/loncapa</source>
@@ -3142,8 +4941,9 @@ file that specifies periodic processes t
 </file>
 <file>
 <source>loncom/ntp/step-tickers</source>
-<target dist='default'>etc/ntp/step-tickers</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/ntp_step-tickers
+</target>
+<categoryname>static conf</categoryname>
 <description>
 file that stimulates running of ntpdate upon init.d/xntpd initiation
 </description>
@@ -3178,7 +4978,7 @@ Controls the launching/halting of lonc,
 </description>
 </file>
 <link>
-<linkto dist='default'>etc/rc.d/init.d/loncontrol</linkto>
+<linkto>etc/rc.d/init.d/loncontrol</linkto>
 <target dist='default'>
 etc/rc.d/rc0.d/K05loncontrol;
 etc/rc.d/rc1.d/K05loncontrol;
@@ -3194,8 +4994,8 @@ symbolic links to /etc/rc.d/init.d/lonco
 </link>
 <file>
 <source>loncom/atalk/config</source>
-<target dist='default'>etc/atalk/config</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/config</target>
+<categoryname>static conf</categoryname>
 <description>
 configuration file to make LON-CAPA server file space accessible to
 Appleshares access (Macintosh)