--- doc/loncapafiles/loncapafiles.lpml	2002/02/06 15:52:35	1.97
+++ doc/loncapafiles/loncapafiles.lpml	2002/08/02 20:08:57	1.155
@@ -1,7 +1,9 @@
+<!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 1.97 2002/02/06 15:52:35 albertel Exp $ -->
+<!-- $Id: loncapafiles.lpml,v 1.155 2002/08/02 20:08:57 harris41 Exp $ -->
 
 <!--
 
@@ -37,7 +39,16 @@ http://www.lon-capa.org/
 
 <lpml>
 <specialnotices>
-<specialnotice dist='redhat7.0 redhat7.1'>
+<specialnotice dist='default'>
+!!! REDHAT 6.2 NOTICE !!!
+!!! Sometimes an incorrect /etc/hosts file is incorrectly generated !!!
+!!! This sometimes happens (bad): !!!
+!!! 127.0.0.1  computer1 localhost.localdomain localhost  !!!
+!!! Should be: !!!
+!!! 127.0.0.1  localhost.localdomain  localhost !!!
+!!! 35.2.3.80  computer1 computer1.notreal.msu.edu !!!
+</specialnotice>
+<specialnotice dist='redhat7 redhat7.1'>
 !!!!!!!!!  REDHAT 7.*   NOTICE   !!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!  LINE IN Cookie.pm     !!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!  MUST BE REPLACED DUE  !!!!!!!!!!!!!!!!!!!!
@@ -183,11 +194,10 @@ Division of Science and Mathematics Educ
   <rpmGroup>Utilities/System</rpmGroup>
   <rpmSource>LON-CAPA-base-3.1.tar.gz</rpmSource>
   <rpmAutoReqProv>no</rpmAutoReqProv>
-  <rpmdescription>This package facilitates a base installation of LON-CAPA files in their directories.\n
-The files in this package are only those directly associated with the network communication\n
-layer established through direct server-to-server communications (via lond and lonc); plus\n
-those which configure (but otherwise not constitute) external software packages like Apache\n
-and Athena-Kerberos.  For more on the LON-CAPA project, visit http://www.lon-capa.org/.</rpmdescription>
+  <rpmdescription>This package facilitates a base installation of LON-CAPA \n
+files in their directories.\n
+For more on the LON-CAPA project, visit http://www.lon-capa.org/.
+  </rpmdescription>
   <rpmpre>echo '***********************************************************************'\n
 echo 'LON-CAPA  LearningOnline with CAPA'\n
 echo 'http://www.lon-capa.org/'\n
@@ -201,121 +211,112 @@ echo 'This installation assumes an insta
 echo ' '\n
 echo 'The server computer should be currently connected to the ethernet'\n
 echo ' '\n
-echo 'The files in this package are only those directly associated with the network communication'\n
-echo 'layer established through direct server-to-server communications (via lond and lonc); plus'\n
-echo 'those which configure (but otherwise not constitute) external software packages like Apache'\n
-echo 'and Athena-Kerberos.'\n
 echo '***********************************************************************'\n
 </rpmpre>
 <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'>
   <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'>
   <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'>
   <targetdir dist='default'>etc/httpd/conf</targetdir>
   <categoryname>standard</categoryname>
   <description>web configuration files</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>etc/ntp</targetdir>
   <categoryname>standard</categoryname>
   <description>configuration directory for network time protocol</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>etc/pam.d</targetdir>
   <categoryname>standard</categoryname>
   <description>configuration directory for password authentication mechanism
   </description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>etc/rc.d/init.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>etc/rc.d/rc0.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>etc/rc.d/rc1.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>etc/rc.d/rc2.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>etc/rc.d/rc3.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>etc/rc.d/rc4.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>etc/rc.d/rc5.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>etc/rc.d/rc6.d</targetdir>
-  <targetdir dist='redhat7.1 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'>
   <targetdir dist='default'>home/httpd/lonTabs</targetdir>
   <categoryname>standard</categoryname>
   <description>tab-formatted reference files</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd</targetdir>
   <categoryname>standard</categoryname>
   <description>start of the web server tree</description>
 </directory>
-<directory>
+<directory dist='default'>
   <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'>
   <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'>
   <targetdir dist='default'>home/httpd/html/lon-status/londchld</targetdir>
   <categoryname>server standard</categoryname>
   <description>
@@ -323,114 +324,158 @@ Used by lond parent to check if children
 (otherwise they are killed and replaced).
   </description>
 </directory>
-<directory>
+<directory dist='default'>
   <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'>
   <targetdir dist='default'>home/httpd/prtspool</targetdir>
   <categoryname>server standard</categoryname>
   <description>for the output of lonprintout.pm
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <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'>
   <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'>
   <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>
+<directory dist='default'>
+  <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'>
+  <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'>
   <targetdir dist='default'>home/httpd/lonIDs</targetdir>
   <categoryname>server standard</categoryname>
   <description>cookie jar</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/sockets</targetdir>
   <categoryname>server standard</categoryname>
   <description>lonc's sockets</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/sockets/delayed</targetdir>
   <categoryname>server standard</categoryname>
   <description>lonc's sockets (delayed)</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/cgi-bin</targetdir>
   <categoryname>standard</categoryname>
   <description>location of cgi scripts</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/html</targetdir>
   <categoryname>server standard</categoryname>
   <description>location of web-accessible file tree</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/html/res</targetdir>
   <categoryname>server standard</categoryname>
   <description>root of resource tree</description>
 </directory>
-<directory>
+<directory dist='default'>
+  <targetdir dist='default'>home/httpd/html/userfiles</targetdir>
+  <categoryname>server standard</categoryname>
+  <description>root for user uploaded files</description>
+</directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/html/adm</targetdir>
   <categoryname>server readonly</categoryname>
   <description>unauthenticated resources</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/html/adm/rat</targetdir>
   <categoryname>server readonly</categoryname>
   <description>home of the rat</description>
 </directory>
-<directory>
+<directory dist='default'>
   <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'>
+  <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'>
+  <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'>
+  <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'>
+  <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'>
+  <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'>
+  <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'>
   <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'>
   <targetdir dist='default'>home/httpd/html/adm/lonIcons</targetdir>
   <categoryname>server readonly</categoryname>
   <description>graphic widgets</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/html/adm/lonMisc</targetdir>
   <categoryname>server readonly</categoryname>
   <description>miscellaneous resources</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>home/httpd/html/adm/lonKaputt</targetdir>
   <categoryname>server readonly</categoryname>
   <description>error warnings and icons</description>
 </directory>
-<directory>
+<directory dist='default'>
   <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.
@@ -438,70 +483,92 @@ 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'>
   <targetdir dist='default'>home/httpd/html/adm/MathML</targetdir>
   <categoryname>server readonly</categoryname>
   <description>mathematics markup language resources</description>
 </directory>
-<directory>
+<directory dist='default'>
   <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'>
   <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'>
   <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'>
   <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'>
   <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'>
   <targetdir dist='default'>home/httpd/html/res/adm/pages/annotations
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description></description>
 </directory>
-<directory>
+<directory dist='default'>
   <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'>
   <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='debian'>usr/local/lib/perl/5.6.0</targetdir>
   <categoryname>standard</categoryname>
   <description>system perl tree (usually present on linux systems)
   </description>
 </directory>
-<directory>
+<directory dist='default'>
+  <targetdir dist='default'>usr/local/loncapa/bin</targetdir>
+  <categoryname>standard</categoryname>
+  <description>local binary files for loncapa</description>
+</directory>
+<directory dist='default'>
+  <targetdir dist='default'>usr/local/loncapa/doc</targetdir>
+  <categoryname>standard</categoryname>
+  <description>local documentation files for loncapa</description>
+</directory>
+<directory dist='default'>
+  <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'>
+  <targetdir dist='default'>usr/local/man/man1</targetdir>
+  <categoryname>standard</categoryname>
+  <description>local manual pages</description>
+</directory>
+<directory dist='default'>
   <targetdir dist='default'>usr/man/man1</targetdir>
   <categoryname>standard</categoryname>
   <description>manual pages</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>usr/man/man3</targetdir>
   <categoryname>standard</categoryname>
   <description>manual pages</description>
 </directory>
-<directory>
+<directory dist='default'>
   <targetdir dist='default'>usr/sbin</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for superuser executables</description>
@@ -536,25 +603,23 @@ 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>
@@ -576,38 +641,22 @@ MySQL database</td></tr>
 </note>
 </file>
 <file>
-<source>loncom/httpd.conf</source>
-<target dist='default'>etc/httpd/conf/httpd.conf</target>
+<source>loncom/loncapa_apache.conf</source>
+<target dist='default'>etc/httpd/conf/loncapa_apache.conf</target>
 <categoryname>static conf</categoryname>
 <description>
-This is the main server configuration file.  The settings here are
-more or less standard for the Apache web server.  Most notably (and
-importantly!), perl handling and mod_perl are enabled in this configuration
-file.
-</description>
-</file>
-<file>
-<source>loncom/srm.conf</source>
-<target dist='default'>etc/httpd/conf/srm.conf</target>
-<categoryname>static conf</categoryname>
-<description>
-<p>
-This file configures the "name space" of the Apache web server.  
-<tt>srm.conf</tt>
-defines when specific perl modules should be called to handle a given
-request.  This definition is a function of both the name of the perl module,
-and a specific regular expression associated with the URL, such as
-"^/res/.*\.page".
-</p>
-<p>
-Here is an example entry:
-<pre>
-&lt;LocationMatch "^/res/.*\.page$&gt;
-SetHandler perl-script
-PerlHandler Apache::lonpage
-&lt;/LocationMatch&gt;
-</pre>
-</p>
+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>
@@ -622,13 +671,18 @@ well as causing the Apache module to be
 </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='run if dependencies change'>
+loncom/thesaurus/build_thesaurus_wrapper.sh
+</build>
+<dependencies>
+rawkey.txt
+</dependencies>
 </file>
 <file>
 <source>loncom/interface/mydesk.tab</source>
@@ -647,6 +701,14 @@ Descriptive list of file extensions, and
 </description>
 </file>
 <file>
+<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.gif</source>
 <target dist='default'>home/httpd/cgi-bin/barcode.gif</target>
 <categoryname>script</categoryname>
@@ -656,6 +718,22 @@ parameter.
 </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>
+<description>
+utility cgi script to view status of cluster
+</description>
+</file>
+<file>
 <source>loncom/cgi/graph.gif</source>
 <target dist='default'>home/httpd/cgi-bin/graph.gif</target>
 <categoryname>script</categoryname>
@@ -668,6 +746,22 @@ GDGraph-1.33 and GDTextUtils-0.80.
 </note>
 </file>
 <file>
+<source>loncom/cgi/lonversions.pl</source>
+<target dist='default'>home/httpd/cgi-bin/lonversions.pl</target>
+<categoryname>script</categoryname>
+<description>
+utility cgi script to view software versions of a remote server
+</description>
+</file>
+<file>
+<source>loncom/cgi/ping.pl</source>
+<target dist='default'>home/httpd/cgi-bin/ping.pl</target>
+<categoryname>script</categoryname>
+<description>
+cgi-script to ping other server
+</description>
+</file>
+<file>
 <source>loncom/cgi/plot.gif</source>
 <target dist='default'>home/httpd/cgi-bin/plot.gif</target>
 <categoryname>script</categoryname>
@@ -720,12 +814,14 @@ blank.library;
 blank.library.meta;
 blank.problem;
 blank.problem.meta;
-formula.problem;
-formula.problem.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;
@@ -740,8 +836,8 @@ 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
 </filenames>
@@ -850,8 +946,7 @@ Basic auth password to access /lon-statu
 </file>
 <file>
 <source>loncom/smb.conf</source>
-<target dist='default'>etc/smb.conf</target>
-<target dist='redhat7.1'>etc/samba/smb.conf</target>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/smb.conf</target>
 <categoryname>conf</categoryname>
 <description>
 configuration file to make LON-CAPA server file space accessible to network
@@ -885,6 +980,14 @@ 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/lonc</source>
 <target dist='default'>home/httpd/perl/lonc</target>
 <categoryname>script</categoryname>
@@ -898,7 +1001,8 @@ 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>
@@ -909,9 +1013,10 @@ loncom/build/pod2man.sh ../lonc > ../../
 <source>doc/scripts/lonc.html</source>
 <target dist='default'>home/httpd/html/adm/help/scripts/lonc.html</target>
 <categoryname>doc</categoryname>
-<description>man page for lonc</description>
+<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>
@@ -928,7 +1033,7 @@ 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,
@@ -942,7 +1047,8 @@ 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>
@@ -953,9 +1059,10 @@ loncom/build/pod2man.sh ../lond > ../../
 <source>doc/scripts/lond.html</source>
 <target dist='default'>home/httpd/html/adm/help/scripts/lond.html</target>
 <categoryname>doc</categoryname>
-<description>man page for lond</description>
+<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>
@@ -986,7 +1093,8 @@ 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>
@@ -997,9 +1105,10 @@ loncom/build/pod2man.sh ../lonsql > ../.
 <source>doc/scripts/lonsql.html</source>
 <target dist='default'>home/httpd/html/adm/help/scripts/lonsql.html</target>
 <categoryname>doc</categoryname>
-<description>man page for lonsql</description>
+<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>
@@ -1036,6 +1145,17 @@ 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>
@@ -1108,14 +1228,15 @@ 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>
@@ -1169,6 +1290,33 @@ 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/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/publisher/loncfile.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/loncfile.pm</target>
 <categoryname>handler</categoryname>
@@ -1179,6 +1327,264 @@ 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/build/buildHelp.sh</build>
+</file>
+<file>
+<source>/doc/help/author.manual.ps</source>
+<target dist='default'>home/httpd/html/adm/help/author.manual.ps</target>
+<categoryname>handler</categoryname>
+<description>
+The rendered Author's 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>handler</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
+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>handler</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
+login.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>handler</categoryname>
+<description>
+Tex files for the help system
+</description>
+<filenames>
+About_Authors_Manual.tex
+About_Numerical_and_Formula_Response.tex
+Ambiguous_Reference.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_Dynamic_Plot.tex
+Authoring_HTML_vs_Tex.tex
+Authoring_M_Tag.tex
+Authoring_Piecewise_Plot.tex
+Calling_Functions.tex
+Coauthor.tex
+Construction_Space_Overview.tex
+Course_Add_Student.tex
+Course_Chart_To_Excel.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_Feedback_Addresses.tex
+Course_Homework_Performance_Overview.tex
+Course_Message_Access.tex
+Course_Problem_Weight.tex
+Course_Setting_Parameters.tex
+Course_Student_Grade_Override.tex
+Course_Student_Work.tex
+Course_Toplevel_Seq.tex
+Creating_A_Course_Intro.tex
+Creating_New_Content_Pages.tex
+Creating_Online_Problems.tex
+Creating_Radio_Response_Problems.tex
+Foils.tex
+Formula_Response_Example.tex
+Formula_Response_Limitations.tex
+Formula_Response_Problems.tex
+Formula_Response_Sampling.tex
+Formula_Tolerance.tex
+How_To_Edit_Existing_Content_Pages.tex
+Latex_Footer.tex
+Latex_Header.tex
+Login_To_LON-CAPA.tex
+Metadata_Description.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
+Problem_Editor_Testing_Area.tex
+Problem_Editor_XML_Index.tex
+Problem_Types.tex
+Publishing_A_Resource.tex
+Publishing_Author_Tutorial_Segue.tex
+Publishing_Copyright.tex
+Publishing_Intro.tex
+Publishing_Keywords.tex
+Radio_Response_Problems.tex
+Radio_Response_Randomization.tex
+Resource_Types.tex
+Script_Tutorial_Intro.tex
+Scripting_Help.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_Alternative_View.tex
+Spreadsheet_Changes_To_Grading.tex
+Spreadsheet_Col_Sum.tex
+Spreadsheet_Completely_Recalc.tex
+Spreadsheet_Empty_Rows.tex
+Spreadsheet_Export_Row.tex
+Spreadsheet_Functions.tex
+Spreadsheet_Import_Values.tex
+Spreadsheet_Levels.tex
+Spreadsheet_Lists.tex
+Spreadsheet_Manual_Title_Page.tex
+Spreadsheet_Max_Depth_Exceeded.tex
+Spreadsheet_OOO_Rows.tex
+Spreadsheet_Op_On_All_Problem_Parts.tex
+Spreadsheet_Parms.tex
+Spreadsheet_Problem_Weight.tex
+Spreadsheet_Ranges.tex
+Spreadsheet_Specifying_Cells.tex
+Spreadsheet_Student_Visible.tex
+Spreadsheet_Symbolic_Names.tex
+Spreadsheet_Template_Row.tex
+Spreadsheet_Ternary_Operator.tex
+Spreadsheet_Tries.tex
+String_Response_Problem_Creation.tex
+String_Response_Problems.tex
+Tolerance.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
+</filenames>
+</fileglob>
+<file>
+<source>loncom/html/adm/help/fragmentLabels.gdbm</source>
+<target dist='default'>home/httpd/html/adm/help/fragmentLabels.gdbm</target>
+<categoryname>handler</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>
@@ -1188,6 +1594,33 @@ 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 Statistcs 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>
+The module that generate the html for the Problem Analysis web pages.
+</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>
@@ -1211,7 +1644,8 @@ 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>
@@ -1219,12 +1653,15 @@ 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>
@@ -1254,7 +1691,8 @@ 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>
@@ -1272,7 +1710,8 @@ Handler to publish directories.
 <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>
@@ -1280,12 +1719,15 @@ 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>
@@ -1307,7 +1749,8 @@ 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>
@@ -1315,12 +1758,16 @@ 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>
@@ -1341,7 +1788,8 @@ 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>
@@ -1349,12 +1797,15 @@ 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>
@@ -1416,11 +1867,19 @@ 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>
+Contains a set of functions that generate html controls and data layouts
+</description>
+</file>
+<file>
+<source>loncom/interface/loncoursedata.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/loncoursedata.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Produces simple LectureOnline-like student assessment performance chart
+Common functions for handling student course data (download and process)
 </description>
 </file>
 <file>
@@ -1439,7 +1898,8 @@ 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>
@@ -1447,12 +1907,15 @@ 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>
@@ -1597,12 +2060,22 @@ 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>
@@ -1610,12 +2083,16 @@ 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>
@@ -1684,7 +2161,8 @@ 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>
@@ -1692,12 +2170,15 @@ 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>
@@ -1729,7 +2210,8 @@ 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>
@@ -1737,12 +2219,16 @@ 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>
@@ -1828,7 +2314,8 @@ 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>
@@ -1836,12 +2323,14 @@ 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>
@@ -1853,7 +2342,7 @@ 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>
@@ -1863,7 +2352,8 @@ 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>
@@ -1871,12 +2361,16 @@ 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>
@@ -1888,7 +2382,7 @@ 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>
@@ -2013,6 +2507,17 @@ handles request to the CAPA homework pro
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/xml/Safe.pm</source>
+<target dist='default'>home/httpd/lib/perl/Safe.pm</target>
+<categoryname>handler</categoryname>
+<description>
+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.pm</target>
 <categoryname>handler</categoryname>
@@ -2039,7 +2544,8 @@ 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>
@@ -2047,12 +2553,14 @@ 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>
@@ -2069,12 +2577,41 @@ 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>
@@ -2082,12 +2619,14 @@ 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>
@@ -2118,7 +2657,8 @@ 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>
@@ -2126,12 +2666,14 @@ 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>
@@ -2185,7 +2727,8 @@ 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>
@@ -2193,12 +2736,14 @@ 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>
@@ -2220,7 +2765,8 @@ 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>
@@ -2228,12 +2774,15 @@ 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>
@@ -2274,7 +2823,8 @@ 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>
@@ -2282,12 +2832,14 @@ 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>
@@ -2521,10 +3073,12 @@ 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;
+accessbutton.gif;
 arrow_up.gif;
 cab.gif;
 cab_big.gif;
@@ -2537,6 +3091,10 @@ 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;
@@ -2545,6 +3103,7 @@ form.gif;
 form_big.gif;
 gif.gif;
 gif_big.gif;
+header.gif;
 htm.gif;
 html.gif;
 html_big.gif;
@@ -2553,14 +3112,19 @@ jar_big.gif;
 jpg.gif;
 jpg_big.gif;
 latex.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;
 meta.gif;
 meta_big.gif;
 mov.gif;
@@ -2598,8 +3162,11 @@ txt.gif;
 txt_big.gif;
 unknown.gif;
 unknown_big.gif;
+upperleft.gif;
+upperright.gif;
 user.gif;
 user_big.gif;
+userauthentication.gif;
 wav.gif;
 wav_big.gif;
 white_space_20_22.gif;
@@ -2625,15 +3192,14 @@ 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;
@@ -2643,7 +3209,7 @@ subm_button.gif
 <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>
+<target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/tth.pm</target>
 <categoryname>system file</categoryname>
 <description>
 perl module for invoking functions specific to TeX-to-HTML conversion
@@ -2657,9 +3223,30 @@ 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/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>
 <categoryname>system file</categoryname>
 <description>
 shared library file for dynamic loading and unloading
@@ -2682,7 +3269,7 @@ modules/TexConvert/tthperl/commands
 <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>
 <categoryname>system file</categoryname>
 <description>
 perl module for invoking functions specific to CAPA
@@ -2697,7 +3284,7 @@ the build process however.
 <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>
 <categoryname>system file</categoryname>
 <description>
 bootstrap file associated with dynamic loading of this module on multiple
@@ -2713,7 +3300,7 @@ the build process however.
 <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>
 <categoryname>system file</categoryname>
 <description>
 shared library file for dynamic loading and unloading
@@ -2723,7 +3310,33 @@ loncom/homework/caparesponse/commands
 </build>
 <dependencies>
 caparesponse.c;
-caparesponse.pm
+caparesponse.pm;
+README;
+Makefile.PL;
+capa.i;
+commands;
+../../../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>
@@ -2793,8 +3406,8 @@ 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>
@@ -2818,14 +3431,26 @@ Define unit prefixing and conversion for
 <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>
+0.gif;
+1.gif;
+2.gif;
+3.gif;
+4.gif;
+5.gif;
+6.gif;
+7.gif;
+8.gif;
+9.gif;
 a.gif;
+anno.gif;
 anot.gif;
 b.gif;
 back.gif;
+bchat.gif;
 bkm.gif;
 brws.gif;
 c.gif;
@@ -2833,12 +3458,14 @@ catalog.gif;
 ccrs.gif;
 chat.gif;
 chrt.gif;
+colon.gif;
 com.gif;
 courses.gif;
 cprv.gif;
 cstr.gif;
 d.gif;
 dempty.gif;
+docs.gif;
 e.gif;
 egrd.gif;
 empty.gif;
@@ -2870,11 +3497,13 @@ mrk.gif;
 n.gif;
 nav.gif;
 next.gif;
+nothumb.gif;
 o.gif;
 p.gif;
 parm.gif;
 pgrd.gif;
 pparm.gif;
+pref.gif;
 prev.gif;
 prt.gif;
 q.gif;
@@ -2886,6 +3515,7 @@ res.gif;
 roles.gif;
 s.gif;
 sbkm.gif;
+slash.gif;
 space.gif;
 spacer.gif;
 sprs.gif;
@@ -2930,10 +3560,11 @@ 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;
@@ -3030,10 +3661,11 @@ 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;
@@ -3064,10 +3696,11 @@ 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;
@@ -3085,40 +3718,49 @@ javascript for handling client-side inte
 </description>
 </file>
 <file>
-<source>loncom/build/loncapaverifypackages</source>
-<target dist='default'>usr/sbin/loncapaverifypackages</target>
-<categoryname>script</categoryname>
+<source>loncom/build/check-rpms</source>
+<target dist='default'>usr/local/loncapa/bin/check-rpms</target>
+<categoryname>root script</categoryname>
 <description>
-checks the system RPMs against what install.lon-capa.org specifies
+compare installed rpms with up-to-date distribution
 </description>
-<status>deprecated</status>
+<status>tested/documented/beta</status>
 </file>
 <file>
-<source>loncom/build/loncaparestoreconfigurations</source>
-<target dist='default'>usr/sbin/loncaparestoreconfigurations</target>
-<categoryname>script</categoryname>
-<description>
-restores .rpmsave files after a LON-CAPA-base upgrade
-</description>
-<status>deprecated</status>
+<source>doc/man/check-rpms.1</source>
+<target dist='default'>usr/local/man/man1/check-rpms.1</target>
+<categoryname>doc</categoryname>
+<description>man page for check-rpms</description>
+<build trigger='always run'>
+loncom/build/pod2man.sh check-rpms &gt; ../../doc/man/check-rpms.1 &amp;&amp; \
+echo 'manifying check-rpms'
+</build>
+<status>beta</status>
+<dependencies>
+../../loncom/build/check-rpms
+</dependencies>
 </file>
 <file>
-<source>loncom/build/loncapaautoupgrade</source>
-<target dist='default'>usr/sbin/loncapaautoupgrade</target>
-<categoryname>script</categoryname>
-<description>
-does all the things to coordinate updating of LON-CAPA base files.  Should be
-used with caution so that you do not lose work
-</description>
-<status>deprecated</status>
+<source>doc/scripts/check-rpms.html</source>
+<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 &gt; ../../doc/scripts/check-rpms.html \
+&amp;&amp; echo 'pod2html checkrpms'
+</build>
+<status>works/unverified</status>
+<dependencies>
+../../loncom/build/check-rpms
+</dependencies>
 </file>
 <file>
-<source>loncom/build/loncapaverify</source>
-<target dist='default'>usr/sbin/loncapaverify</target>
+<source>loncom/build/loncaparestoreconfigurations</source>
+<target dist='default'>usr/sbin/loncaparestoreconfigurations</target>
 <categoryname>script</categoryname>
 <description>
-makes verification report using loncapaverifypackages and
-loncapaverifybasepackage
+restores .rpmsave files after a LON-CAPA-base upgrade
 </description>
 <status>deprecated</status>
 </file>
@@ -3168,7 +3810,7 @@ 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;
@@ -3184,7 +3826,7 @@ symbolic links to /etc/rc.d/init.d/lonco
 </link>
 <file>
 <source>loncom/atalk/config</source>
-<target dist='default'>etc/atalk/config</target>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/config</target>
 <categoryname>conf</categoryname>
 <description>
 configuration file to make LON-CAPA server file space accessible to