--- doc/loncapafiles/loncapafiles.lpml	2004/07/22 16:17:42	1.382
+++ doc/loncapafiles/loncapafiles.lpml	2005/12/20 16:25:53	1.467
@@ -2,7 +2,7 @@
  "http://lpml.sourceforge.net/DTD/lpml.dtd">
 <!-- loncapafiles.lpml -->
 
-<!-- $Id: loncapafiles.lpml,v 1.382 2004/07/22 16:17:42 www Exp $ -->
+<!-- $Id: loncapafiles.lpml,v 1.467 2005/12/20 16:25:53 www Exp $ -->
 
 <!--
 
@@ -39,7 +39,6 @@ http://www.lon-capa.org/
 <lpml>
 <specialnotices>
 <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  !!!
@@ -47,22 +46,6 @@ 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 redhat7.1'>
-!!!!!!!!!  REDHAT 7.*   NOTICE   !!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!  LINE IN Cookie.pm     !!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!  MUST BE REPLACED DUE  !!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!  TO PERL 5.6.0 ERROR   !!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!                        !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!! The offending line is in CGI/Cookie.pm                           !!
-!!!!                                                                  !!
-!!!! it should be changed from                                        !!
-!!!! $path   = CGI::url(-absolute=>1) unless defined $path;           !!
-!!!! to                                                               !!
-!!!! ($path = $ENV{'SCRIPT_NAME'})=~s![^/]+$!! unless $path;          !!
-!!!!                                                                  !!
-!!!! (This is just below the following line )                         !!
-!!!! # IE requires the path and domain to be present for some reason. !!
-</specialnotice>
 </specialnotices>
 <targetroot>/</targetroot>
 <sourceroot>/home/user/loncapa/</sourceroot>
@@ -336,6 +319,12 @@ echo '**********************************
   <description>perl scripts for managing the LON-CAPA system</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/perl/debug</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>perl scripts for debugging the LON-CAPA system</description>
+</directory>
+<directory dist='default'>
   <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/perl/logs</targetdir>
   <categoryname>server standard</categoryname>
@@ -437,6 +426,12 @@ extensions</description>
 </directory>
 <directory dist='default'>
   <protectionlevel>never_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/cgi-bin/mimetexcache</targetdir>
+  <categoryname>server standard</categoryname>
+  <description>location of cgi scripts</description>
+</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>
@@ -521,6 +516,12 @@ extensions</description>
 </directory>
 <directory dist='default'>
   <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/fonts</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>fonts</description>
+</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>
@@ -533,6 +534,24 @@ extensions</description>
 </directory>
 <directory dist='default'>
   <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/jmol</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Jmol files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/jsMath</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>jsMath support files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/jsMath/plugins</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>jsMath plugin 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>
@@ -1248,6 +1267,7 @@ fullscreen.html;
 old-fullscreen.html;
 select_color.html;
 popup.js;
+link.html;
 </filenames>
 </fileglob>
 <fileglob>
@@ -1360,7 +1380,11 @@ SimpleMatching.problem.meta;
 SimpleRank.problem;
 SimpleRank.problem.meta;
 SimpleTrueFalse.problem;
-SimpleTrueFalse.problem.meta
+SimpleTrueFalse.problem.meta;
+organic.problem;
+organic.problem.meta;
+reaction.problem;
+reaction.problem.meta
 </filenames>
 </fileglob>
 <file>
@@ -1525,6 +1549,14 @@ Batch script for removing temporary tabl
 </description>
 </file>
 <file>
+<source>loncom/metadata_database/parse_activity_log.pl</source>
+<target dist='default'>home/httpd/perl/parse_activity_log.pl</target>
+<categoryname>script</categoryname>
+<description>
+Batch script to copy activy logs from native format into the SQL metadata database.
+</description>
+</file>
+<file>
 <source>loncom/misc/cleanup_file_caches.pl</source>
 <target dist='default'>home/httpd/perl/cleanup_file_caches.pl</target>
 <categoryname>script</categoryname>
@@ -1543,6 +1575,15 @@ nohist_accesscount.db.
 </description>
 </file>
 <file>
+<source>loncom/debugging_tools/modify_config_files.pl</source>
+<target dist='default'>home/httpd/perl/modify_config_files.pl</target>
+<categoryname>script</categoryname>
+<description>
+Batch script to ensure certain LONCAPA configuration parameters for yum and
+MySQL are included in their configuration files.
+</description>
+</file>
+<file>
 <source>loncom/lonhttpd</source>
 <target dist='default'>home/httpd/perl/lonhttpd</target>
 <categoryname>script</categoryname>
@@ -1551,6 +1592,22 @@ Small fry httpd on port 8080
 </description>
 </file>
 <file>
+<source>loncom/lonmemcached</source>
+<target dist='default'>home/httpd/perl/lonmemcached</target>
+<categoryname>script</categoryname>
+<description>
+small script to handle the start up of the memcached daemon
+</description>
+</file>
+<file>
+    <source>loncom/request_ssl_key.sh</source>
+    <target dist='default'>home/httpd/lonCerts/request_ssl_key.sh</target>
+    <categoryname>script</categoryname>
+    <description>
+        Script that requests a Lon-CAPA ssl key.
+    </description>
+</file>
+<file>
 <source>loncom/lonc</source>
 <target dist='default'>home/httpd/perl/lonc</target>
 <categoryname>script</categoryname>
@@ -1633,10 +1690,19 @@ echo 'pod2html lond'
 </dependencies>
 </file>
 <file>
-<source>loncom/build/CHECKRPMS</source>
+<source dist='default'>loncom/build/CHECKRPMS.default</source>
+<source dist='fedora1 fedora2 fedora3 fedora4'>loncom/build/CHECKRPMS.fedora</source>
+<source dist='rhes4'>loncom/build/CHECKRPMS.rhel</source>
+<source dist='suse9.2 suse9.3 sles9'>loncom/build/CHECKRPMS.suse</source>
 <target dist='default'>home/httpd/cgi-bin/CHECKRPMS</target>
 <categoryname>script</categoryname>
 <description>CGI script that checks status of RPMs</description>
+<dependencies>
+loncom/build/CHECKRPMS.default;
+loncom/build/CHECKRPMS.fedora;
+loncom/build/CHECKRPMS.rhel;
+loncom/build/CHECKRPMS.suse;
+</dependencies>
 </file>
 <file>
 <source>loncom/cgi/loncron.pl</source>
@@ -2003,6 +2069,15 @@ Handler to put up syllabus
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonrss.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonrss.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for adding to and displaying RSS
+</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>
@@ -2118,6 +2193,15 @@ packages into construction space, or int
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/imspackages/imsexport.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/imsexport.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Routines used in londocs to export templated files to an IMS package.
+</description>
+<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>
@@ -2426,15 +2510,16 @@ all_functions_table.tex;
 adaptive_hints.tex;
 Additional_Help.tex;
 Ambiguous_Reference.tex;
-Analysis_Analyze_as.tex;
 Analysis_Analyze_Over.tex;
-Analysis_num_plots.tex;
 Analyze_Problem.tex;
+Answer_Date.tex;
 Annotation.tex;
 Authentication.tex;
+Auth_Options.tex;
 Authoring_Adding_Pictures.tex;
 Authoring_DataResponse.tex;
 Authoring_Dynamic_Plot_Axes.tex;
+Authoring_Dynamic_Plot_Color_Selection.tex;
 Authoring_Dynamic_Plot_Curve_Data.tex;
 Authoring_Dynamic_Plot_Curve_Function.tex;
 Authoring_Dynamic_Plot_Curve.tex;
@@ -2470,6 +2555,7 @@ Author_Manual_Title_Page.tex;
 Author_Numerical_and_Formula.tex;
 Author_Remote_Control.tex;
 Bookmarks.tex;
+Browsing_Resources.tex;
 Bugzilla.tex;
 Caching.tex;
 Calendar_Add_Announcement.tex;
@@ -2477,17 +2563,23 @@ Calendar_Remove_Announcement.tex;
 Calling_Functions.tex;
 CAPA_LON-CAPA_function_diffs.tex;
 Cascading_Parameters.tex;
+Catalog_Info.tex;
 Change_Colors.tex;
 Change_Password.tex;
 Chart_Description.tex;
 Change_Discussion_Display.tex;
+Chart_Enrollment_Status.tex;
 Chart_Output_Data.tex;
 Chart_Output_Formats.tex;
+Chart_Sections.tex;
+Chart_Sequences.tex;
+Chart_Student_Data.tex;
 Chatting.tex;
 Coauthor.tex;
 Construction_Space_Overview.tex;
 Course_Add_Other.tex;
 Course_Add_Student.tex;
+Course_Automated_Enrollment.tex;
 Course_Broadcast_Message.tex;
 Course_Change_Privileges.tex;
 Course_Chart_To_Excel.tex;
@@ -2501,6 +2593,7 @@ Course_Discussion_Board.tex;
 Course_Drop_Student.tex;
 Course_Edit_Content.tex;
 Course_Editing_Custom_Roles.tex;
+Course_Environment.tex;
 Course_Extending_Due_Dates.tex;
 Course_Face_To_Face_Records.tex;
 Course_Feedback_Addresses.tex;
@@ -2511,6 +2604,7 @@ Course_Maximum_Collaborators.tex;
 Course_Message_Access.tex;
 Course_Modify_Student_Data.tex;
 Course_Parameter_Levels.tex;
+Course_Parameter_Table_Mode.tex;
 Course_Problem_Weight.tex;
 Course_Set_Start_End_Date.tex;
 Course_Setting_Parameters.tex;
@@ -2527,6 +2621,7 @@ Creating_Online_Problems.tex;
 Creating_Radio_Response_Problems.tex;
 Developer_Manual_Title_Page.tex;
 Developer_Tutorial.tex;
+Distribute_Messages.tex;
 Docs_About_Bulletin_Board.tex;
 Docs_About_My_Personal_Info.tex;
 Docs_About_Simple_Page.tex;
@@ -2534,11 +2629,13 @@ Docs_About_Syllabus.tex;
 Docs_Adding_Course_Doc.tex;
 Docs_Adding_External_Resource.tex;
 Docs_Adding_Folders.tex;
+Docs_Adding_Pages.tex;
 Docs_Adding_Syllabus.tex;
 Docs_Alternatives.tex;
 Docs_Check_Resource_Versions.tex;
 Docs_Creating_From_Template.tex;
 Docs_Dump_Course_Docs.tex;
+Docs_Export_Course_Docs.tex;
 Docs_Editing_Templated_Pages.tex;
 Docs_Essay.tex;
 Docs_Importing_LON-CAPA_Resource.tex;
@@ -2555,9 +2652,15 @@ Docs_String_Response.tex;
 Docs_Supplemental.tex;
 Docs_Uploading_From_Harddrive.tex;
 Docs_Verify_Content.tex;
+Due_Date.tex;
 Edit_Syllabus.tex;
 exam_basics.tex;
 Exploring_Your_Course.tex;
+Feedback_Author.tex;
+Feedback_Content.tex;
+Feedback_Discuss_Anon.tex;
+Feedback_Discussion.tex;
+Feedback_Policy.tex;
 Finding_Resources.tex;
 Foils.tex;
 Formula_Response_Adv_Intro.tex;
@@ -2568,6 +2671,13 @@ Formula_Response_Sampling.tex;
 Formula_Tolerance.tex;
 General_Intro.tex;
 Generation.tex;
+Grade_All.tex;
+Grade_Intro.tex;
+Grade_One.tex;
+Grade_Scantron.tex;
+Grade_Sequence.tex;
+Grade_Upload.tex;
+Grade_Verify.tex;
 GradingOptions.tex;
 Greek_Symbols.tex;
 Guts_Apache_Env.tex;
@@ -2601,6 +2711,7 @@ Numerical_Response_Simple_Example.tex;
 Numerical_Response_Tutorial_A.tex;
 Numerical_Response_Units.tex;
 numerical_wrong_answers.tex;
+Open_Date.tex;
 Option_Response_Concept_Group_Example.tex;
 Option_Response_Matching_Example.tex;
 Option_Response_Problem_Creation.tex;
@@ -2609,6 +2720,8 @@ Option_Response_Problem_Parts.tex;
 Option_Response_Problems.tex;
 Option_Response_Simple.tex;
 Other_Symbols.tex;
+Parameter_Helper.tex;
+Parameter_Overview.tex;
 Part_Tag_Edit_Help.tex;
 Personal_Info_Page.tex;
 Physical_Units.tex;
@@ -2616,16 +2729,22 @@ Prefs_About_Me.tex;
 Prefs_Forwarding.tex;
 Prefs_Language.tex;
 Prefs_Screen_Name_Nickname.tex;
+Print_Library.tex;
+Print_Options.tex;
 Print_Resource.tex;
+Print_Tricks.tex;
 Problem_Editor_Testing_Area.tex;
 Problem_Editor_XML_Index.tex;
 Problem_LON-CAPA_Functions.tex;
+Problem_LON-CAPA_Image_Options.tex;
+Problem_Parameters.tex;
 Problem_Types.tex;
 Publishing_A_Resource.tex;
 Publishing_Author_Tutorial_Segue.tex;
 Publishing_Copyright.tex;
 Publishing_Intro.tex;
 Publishing_Keywords.tex;
+Quick_Grades_Description.tex;
 Quick_Grades_Possibly_Correct.tex;
 Radio_Response_Problems.tex;
 Radio_Response_Randomization.tex;
@@ -2680,8 +2799,18 @@ Statistics_Sequence.tex;
 Statistics_Cache.tex;
 String_Response_Problem_Creation.tex;
 String_Response_Problems.tex;
+Submission_Time_Analysis.tex;
 Syllabus_ExtLink.tex;
 Syllabus_URLs.tex;
+Table_Mode.tex;
+TEXDropEmptyColumns_attribute.tex;
+TEXitemgroupwidth_attribute.tex;
+TEXitemgroup_attribute.tex;
+TEXlayout_attribute.tex;
+TEXsize_attribute.tex;
+TEXtype_attribute.tex;
+TEXwidth_attribute.tex;
+Tries.tex;
 Tolerance.tex;
 Uploaded_Templates_PublicView.tex;
 Uploaded_Templates_TextBoxes.tex;
@@ -2690,6 +2819,8 @@ Variables_in_Scripts.tex;
 Variables_in_the_Answer_Block.tex;
 Variables_in_the_Text_Block.tex;
 Variable_Tutorial_A.tex;
+View_All_Messages.tex;
+View_Critical_Messages.tex;
 What_Is_LON-CAPA.tex;
 Why_LON-CAPA.tex;
 </filenames>
@@ -2727,6 +2858,25 @@ A gdbm file containing a label->tex file
 </description>
 <status>works/unverified</status>
 </file>
+<fileglob>
+  <glob>*</glob>
+  <sourcedir>loncom/html/adm/fonts/</sourcedir>
+  <targetdir dist='default'>home/httpd/html/adm/fonts/</targetdir>
+  <categoryname>interface file</categoryname>
+  <description>
+    Fonts for convertjme.pl
+  </description>
+  <filenames>
+AUTHORS;
+BUGS;
+DejaVuSerif-Roman.ttf;
+LICENSE;
+NEWS;
+README;
+status.txt;
+unicover.txt
+  </filenames>
+</fileglob>
 <file>
 <source>loncom/interface/lonstatistics.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonstatistics.pm</target>
@@ -2746,6 +2896,15 @@ Utility module for statistics and data m
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lontrackstudent.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lontrackstudent.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to parse and analyze activity.log
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/statistics/lonproblemstatistics.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonproblemstatistics.pm
 </target>
@@ -2823,6 +2982,16 @@ The module that generate the html for th
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonwhatsnew.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonwhatsnew.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to display items in course requiring action.
+</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>
@@ -2908,6 +3077,15 @@ tag handlers needed by externalresponse.
 <status>works/unverified</status>
 </file>
 <file>
+  <source>loncom/homework/gradesubmission.pl</source>
+  <target dist='default'>home/httpd/cgi-bin/gradesubmission.pl</target>
+  <categoryname>handler</categoryname>
+  <description>
+Example script for use with external response.
+  </description>
+  <status>works/unverified</status>
+</file>
+<file>
 <source>loncom/publisher/lonpubdir.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonpubdir.pm</target>
 <categoryname>handler</categoryname>
@@ -2963,6 +3141,15 @@ Handler to retrieve old versions from re
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/publisher/loncleanup.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/loncleanup.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to clean up HTML files.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>doc/man/Apache__lonretrieve.3</source>
 <target dist='default'>usr/man/man3/Apache::lonretrieve.3</target>
 <categoryname>doc</categoryname>
@@ -3136,6 +3323,7 @@ ru.pm;
 fa.pm;
 ar.pm;
 es.pm;
+x_chef.pm;
 </filenames>
 </fileglob>
 <file>
@@ -3246,6 +3434,23 @@ smiles.gif
   </filenames>
 </fileglob>
 
+<fileglob>
+  <glob>*.*</glob>
+  <sourcedir>loncom/html/adm/jmol/</sourcedir>
+  <targetdir dist='default'>home/httpd/html/adm/jmol/</targetdir>
+  <categoryname>interface file</categoryname>
+  <description>
+    Jmol files, for displaying structures
+  </description>
+  <filenames>
+COPYRIGHT.txt;
+JmolApplet.jar;
+Jmol.js;
+LICENSE.txt;
+README.txt
+  </filenames>
+</fileglob>
+
 <file>
   <source>loncom/homework/convertjme.pl</source>
   <target dist='default'>home/httpd/cgi-bin/convertjme.pl</target>
@@ -3255,6 +3460,62 @@ smiles.gif
   </description>
 </file>
 
+<fileglob>
+  <glob>*.*</glob>
+  <sourcedir>loncom/html/adm/jsMath/</sourcedir>
+  <targetdir dist='default'>home/httpd/html/adm/jsMath/</targetdir>
+  <categoryname>interface file</categoryname>
+  <description>
+jsMath is a Javascript solution to converting TeX to something the browser can see
+  </description>
+  <filenames>
+black.gif;
+blank.gif;
+COPYING.txt;
+jsMath-fallback-mac.js;
+jsMath-fallback-mac-mozilla.js;
+jsMath-fallback-mac-msie.js;
+jsMath-fallback-pc.js;
+jsMath-fallback-symbols.js;
+jsMath-fallback-unix.js;
+jsMath.js;
+jsMath-mozilla.js;
+jsMath-msie-mac.js;
+  </filenames>
+</fileglob>
+
+<file>
+  <source>loncom/html/adm/jsMath/jsMath-fonts-1.2.zip</source>
+  <target dist='default'>home/httpd/html/adm/jsMath/fonts/</target>
+  <categoryname>script</categoryname>
+  <description>
+    Dynamically converts JME strings into either a png or ps file.
+  </description>
+  <installscript>
+commands /home/httpd/html/adm/jsMath
+  </installscript>
+  <dependencies>
+loncom/html/adm/jsMath/commands;
+loncom/html/adm/jsMath/jsMath-fonts-1.2.zip;
+  </dependencies>
+</file>
+
+<fileglob>
+  <glob>*.*</glob>
+  <sourcedir>loncom/html/adm/jsMath/plugins/</sourcedir>
+  <targetdir dist='default'>home/httpd/html/adm/jsMath/plugins/</targetdir>
+  <categoryname>interface file</categoryname>
+  <description>
+jsMath is a Javascript solution to converting TeX to something the browser can see
+  </description>
+  <filenames>
+autoload.js;
+mimeTeX.js;
+noImageFonts.js;
+tex2math.js;
+  </filenames>
+</fileglob>
+
 <file>
 <source>loncom/interface/lontest.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lontest.pm</target>
@@ -3275,15 +3536,6 @@ Handles multiple-choice style responses.
 <status>works/unverified</status>
 </file>
 <file>
-<source>loncom/interface/lonassignments.pm</source>
-<target dist='default'>home/httpd/lib/perl/Apache/lonassignments.pm</target>
-<categoryname>handler</categoryname>
-<description>
-Handles processing of assignments.
-</description>
-<status>works/unverified</status>
-</file>
-<file>
 <source>loncom/interface/loncommunicate.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/loncommunicate.pm</target>
 <categoryname>handler</categoryname>
@@ -3391,6 +3643,24 @@ Course initialization helper.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/html/adm/helper/resettimes.helper</source>
+<target dist='default'>home/httpd/html/adm/helper/resettimes.helper</target>
+<categoryname>handler</categoryname>
+<description>
+Helper to resetting a student's first access time.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+  <source>loncom/html/adm/helper/newslot.helper</source>
+  <target dist='default'>home/httpd/html/adm/helper/newslot.helper</target>
+  <categoryname>handler</categoryname>
+  <description>
+Slot creation and editing 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>
@@ -3505,6 +3775,16 @@ Allows users (including students) to vie
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/loncoursegroups.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/loncoursegroups.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Allows course coordinators to create groups, modify existing groups (including    
+adding, expiring or deleting group members, or modifying group member privileges.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/lonmsg.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonmsg.pm</target>
 <categoryname>handler</categoryname>
@@ -3581,7 +3861,16 @@ Defines the specifics of the assessment
 <target dist='default'>home/httpd/lib/perl/Apache/lonparmset.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Handler to resolve ambiguous file locations
+Handler for setting and modifying both course preferences and coure parameters
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/slotrequest.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/slotrequest.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for students to add access slots
 </description>
 <status>works/unverified</status>
 </file>
@@ -3709,6 +3998,15 @@ Builds up frame set and loads in the rig
 <status>works/unverified</status>
 </file>
 <file>
+<source>rat/lonratmenu.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonratmenu.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Creates horizontal menubar in advanced RAT
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/html/res/adm/pages/homeworkmenu.html</source>
 <target dist='default'>home/httpd/html/res/adm/pages/homeworkmenu.html</target>
 <categoryname>handler</categoryname>
@@ -3994,6 +4292,15 @@ resources
 <status>works/unverified</status>
 </file>
 <file>
+  <source>loncom/homework/bridgetask.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/bridgetask.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+implements the tags for supporting bridge tasks
+  </description>
+  <status>works/unverified</status>
+</file>
+<file>
 <source>loncom/homework/response.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/response.pm</target>
 <categoryname>handler</categoryname>
@@ -4235,6 +4542,27 @@ loncom/build/pod2html.sh ../auth/loncacc
 <status>works/unverified</status>
 </file>
 <file>
+  <source>loncom/auth/migrateuser.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/migrateuser.pm</target>
+  <categoryname>handler</categoryname>
+  <description>auto logsin a remote user</description>
+  <status>works/unverified</status>
+</file>
+<file>
+  <source>loncom/auth/switchserver.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/switchserver.pm</target>
+  <categoryname>handler</categoryname>
+  <description>Setups the transfer of a user between servers</description>
+  <status>works/unverified</status>
+</file>
+<file>
+  <source>loncom/auth/checkauthen.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/checkauthen.pm</target>
+  <categoryname>handler</categoryname>
+  <description>Checks if a user's cookie exists and is valid</description>
+  <status>works/unverified</status>
+</file>
+<file>
 <source>loncom/lonnet/perl/lonrep.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonrep.pm</target>
 <categoryname>handler</categoryname>
@@ -4412,12 +4740,12 @@ loncom/build/pod2html.sh ../lonnet/perl/
 <categoryname>interface file</categoryname>
 <description>Bookmark and tab icon</description>
 </file>
-<link>
-<linkto>etc/mime.types</linkto>
+<file>
+<source>loncom/mime.types</source>
 <target dist='default'>etc/httpd/conf/mime.types</target>
-<categoryname>symbolic link</categoryname>
-<description>symbolic link to /etc/mime.types</description>
-</link>
+<categoryname>www static conf</categoryname>
+<description>Expaned mime.types</description>
+</file>
 <link>
 <linkto>home/httpd/html/res</linkto>
 <target dist='default'>home/httpd/html/raw</target>
@@ -4467,11 +4795,11 @@ Parameter input window.
 </description>
 </file>
 <file>
-<source>rat/client/code.html</source>
-<target dist='default'>home/httpd/html/adm/rat/code.html</target>
+<source>rat/client/ratcode.js</source>
+<target dist='default'>home/httpd/html/res/adm/includes/ratcode.js</target>
 <categoryname>interface file</categoryname>
 <description>
-javascript
+javascript for horizontal menubar in RAT
 </description>
 </file>
 <file>
@@ -4704,6 +5032,9 @@ frowny.gif;
 gif.gif;
 gif_big.gif;
 header.gif;
+header.png;
+helpdesk.gif;
+helpgateway.gif;
 hrrm.gif;
 htm.gif;
 html.gif;
@@ -4739,6 +5070,7 @@ mov_big.gif;
 move_up.gif;
 move_down.gif;
 navmap.correct.gif;
+navmap.partial.gif;
 navmap.ellipsis.gif;
 navmap.open.gif;
 navmap.page.open.gif;
@@ -4781,6 +5113,8 @@ srvhalf.gif;
 srvnull.gif;
 survey.gif;
 survey_big.gif;
+task.gif;
+task_big.gif;
 tex.gif;
 tex_big.gif;
 tth.gif;
@@ -4841,8 +5175,16 @@ subm_button.gif
 </filenames>
 </fileglob>
 <file>
+<source>loncom/xml/algebra/AlgParser.pm</source>
+<target dist='default'>home/httpd/lib/perl/AlgParser.pm</target>
+<categoryname>system file</categoryname>
+<description>
+perl module for invoking functions specific to Algebra-to-TeX-to-HTML conversion
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <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>
@@ -4962,7 +5304,6 @@ Configuration file editing module
 </file>
 <file>
 <source>modules/TexConvert/tthperl/tth.so</source>
-<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>
@@ -4974,18 +5315,18 @@ CVS users.  (You can safely rely on the
 present on your system... don't worry about warnings
 related to this file during the build process.)
 </note>
-<build trigger='run if dependencies change'>
+<build trigger='always run'>
 modules/TexConvert/tthperl/commands
 </build>
 <status>works/unverified</status>
-<privatedependencies>
-../tthdynamic/tthfunc.c;
-../ttmdynamic/ttmfunc.c
-</privatedependencies>
+<dependencies>
+commands;
+compiles/tth.so.i386;
+compiles/tth.so.x86_64
+</dependencies>
 </file>
 <file>
 <source>loncom/homework/caparesponse/capa.pm</source>
-<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>
@@ -5000,7 +5341,6 @@ the build process however.
 </file>
 <file>
 <source>loncom/homework/caparesponse/capa.bs</source>
-<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>
@@ -5016,7 +5356,6 @@ the build process however.
 </file>
 <file>
 <source>loncom/homework/caparesponse/capa.so</source>
-<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>
@@ -5057,6 +5396,28 @@ commands;
 ../../../CAPA/pProj/lex_debug.h
 </dependencies>
 </file>
+<file>
+<source>loncom/cgi/mimeTeX/mimetex.cgi</source>
+<target dist='default'>home/httpd/cgi-bin/mimetex.cgi</target>
+<categoryname>script</categoryname>
+<description>
+cgi binary for doing TeX -> math translation
+</description>
+<build trigger='always run'>
+loncom/cgi/mimeTeX/commands
+</build>
+<dependencies>
+commands;
+gfuntype.c;
+gifsave.c;
+mimetex.c;
+mimetex.h;
+mimetex.html;
+README;
+texfonts.h;
+LICENSE;
+</dependencies>
+</file>
 <fileglob>
 <glob>*.ent</glob>
 <sourcedir>loncom/MathML/</sourcedir>
@@ -5168,6 +5529,11 @@ student.jpg;
 <description>Logos of LON-CAPA domains (jpg)</description>
 <filenames>
 headermsu.jpg;
+headertccfl.jpg;
+header_fsu.jpg;
+header_fsuK12.jpg;
+headerhope.jpg;
+jmsbanner.jpg;
 </filenames>
 </fileglob>
 <fileglob>
@@ -5200,8 +5566,12 @@ unihalle.gif;
 wscc.gif;
 cps.gif;
 fsu.gif;
+fsuK12.gif;
+hope.gif;
+vcu.gif;
 lsd.gif;
 msu.gif;
+jms.gif;
 nsdl.gif;
 pmm.gif;
 sunysb.gif;
@@ -5211,6 +5581,7 @@ fvl.gif;
 csm.gif;
 nau.gif;
 nagoya.gif;
+kanazawa.gif;
 colorado.gif;
 acadiau.gif;
 psuerie.gif;
@@ -5218,6 +5589,9 @@ redford.gif;
 huji.gif;
 ifusp.gif;
 ucsc.gif;
+uiuc.gif;
+uiucheader.gif;
+koinonia.gif;
 waverly.gif;
 cmich.gif;
 UNICAMP.gif;
@@ -5227,8 +5601,14 @@ glps.gif;
 BCHS.gif;
 headersfu.gif;
 uwsp.gif;
+tccfl.gif;
 bsu.gif;
 wmston.gif;
+headerharvard.gif;
+harvard.gif;
+uga.gif;
+headeruga.gif;
+covenantchristianhs.gif;
 </filenames>
 </fileglob>
 <fileglob>
@@ -5245,20 +5625,31 @@ csm.tab;
 huji.tab;
 nau.tab;
 nagoya.tab;
+koinonia.tab;
+kanazawa.tab;
 colorado.tab;
 acadiau.tab;
 psuerie.tab;
 redford.tab;
 cmich.tab;
 ifusp.tab;
+jms.tab;
 ucsc.tab;
+uiuc.tab;
 UNICAMP.tab;
 lakefenton.tab;
 grandblanc.tab;
 fsu.tab;
+fsuK12.tab;
+hope.tab;
+vcu.tab;
 sfu.tab;
 wmston.tab;
 worf.tab;
+tccfl.tab;
+harvard.tab;
+uga.tab;
+tmcc.tab;
 </filenames>
 </fileglob>
 <fileglob>
@@ -5381,10 +5772,12 @@ catalog.gif;
 ccrs.gif;
 chat.gif;
 chrt.gif;
+clst.gif;
 com.gif;
 courses.gif;
 cprv.gif;
 cstr.gif;
+del.gif;
 dempty.gif;
 docs.gif;
 egrd.gif;
@@ -5395,6 +5788,7 @@ fdbk.gif;
 feedback.gif;
 forw.gif;
 grds.gif;
+grps.gif;
 group.gif;
 help.gif;
 info.gif;
@@ -5404,24 +5798,31 @@ ledgreen.gif;
 ledoff.gif;
 ledon.gif;
 ledsend.gif;
+list.gif;
 logout.gif;
+mail.gif;
 mcrs.gif;
 mrk.gif;
 nav.gif;
+new.gif;
 next.gif;
 nothumb.gif;
 parm.gif;
 pgrd.gif;
+port.gif;
 pparm.gif;
 pref.gif;
 prev.gif;
 prt.gif;
+pub.gif;
 qempty.gif;
 reload.gif;
 remotebg.gif;
 res.gif;
 roles.gif;
+rtrv.gif;
 sbkm.gif;
+sctr.gif;
 spacer.gif;
 sprs.gif;
 src.gif;
@@ -5432,6 +5833,14 @@ vbkm.gif;
 </filenames>
 </fileglob>
 <file>
+<source>loncom/html/res/adm/pages/math_example.tex</source>
+<target dist='default'>home/httpd/html/res/adm/pages/math_example.tex</target>
+<categoryname>interface file</categoryname>
+<description>
+ file with an example math equation in it.
+</description>
+</file>
+<file>
 <source>loncom/html/res/adm/pages/imgmaps.html</source>
 <target dist='default'>home/httpd/html/res/adm/pages/imgmaps.html</target>
 <categoryname>interface file</categoryname>
@@ -5632,9 +6041,8 @@ javascript for handling client-side inte
 </description>
 </file>
 <file>
-<source dist='default'>loncom/build/CHECKRPMS</source>
-<source dist='fedora1'>loncom/build/CHECKRPMS.fedora</source>
-<source dist='fedora2'>loncom/build/CHECKRPMS.fedora</source>
+<source dist='default'>loncom/build/CHECKRPMS.default</source>
+<source dist='fedora1 fedora2 fedora3 fedora4'>loncom/build/CHECKRPMS.fedora</source>
 <target dist='default'>usr/local/loncapa/bin/CHECKRPMS</target>
 <categoryname>system script</categoryname>
 <description>
@@ -5739,6 +6147,7 @@ file that allows setuid password privile
 <file>
 <source>loncom/init.d/loncontrol</source>
 <target dist='default'>etc/rc.d/init.d/loncontrol</target>
+<target dist='suse9.2 suse9.3 sles9'>etc/init.d/loncontrol</target>
 <categoryname>root script</categoryname>
 <description>
 Controls the launching/halting of lonc, lond, and lonsql processes.
@@ -5769,6 +6178,15 @@ Appleshares access (Macintosh)
 </description>
 </file>
 <file>
+  <source>loncom/interface/lonnotify.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/lonnotify.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+    Interface for Domain Coordinators to (a) send broadcast e-mail to groups 
+of users, and (b) to display e-mail of this type sent in the past.
+  </description>
+</file>
+<file>
   <source>loncom/interface/lonhelpmenu.pm</source>
   <target dist='default'>home/httpd/lib/perl/Apache/lonhelpmenu.pm</target>
   <categoryname>handler</categoryname>
@@ -5833,5 +6251,71 @@ Appleshares access (Macintosh)
     Local handler for automated enrollment, standard version.
   </description>
 </file>
+<file>
+  <source>loncom/auth/localstudentphoto.pm</source>
+  <target dist='default'>home/httpd/lib/perl/localstudentphoto.pm</target>
+  <categoryname>conf</categoryname>
+  <description>
+    Local handler for automated enrollment.
+  </description>
+</file>
+<file>
+  <source>loncom/auth/localstudentphoto.pm</source>
+  <target dist='default'>home/httpd/lib/perl/localstudentphoto-std.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+    Local handler for automated enrollment, standard version.
+  </description>
+</file>
+<file>
+  <source>loncom/automation/batchcreatecourse.pm</source>
+  <target dist='default'>home/httpd/lib/perl/LONCAPA/batchcreatecourse.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+    Handler for batch creation of courses.
+  </description>
+</file>
+<file>
+  <source>loncom/automation/Autocreate.pl</source>Autocreate.pl
+  <target dist='default'>home/httpd/perl/Autocreate.pl</target>
+  <categoryname>script</categoryname>
+  <description>
+    Script for automated course creation.
+  </description>
+</file>
+<fileglob>
+    <glob>*</glob>
+    <sourcedir>loncom/debugging_tools/</sourcedir>
+    <targetdir dist='default'>home/httpd/perl/debug/</targetdir>
+    <categoryname>script</categoryname>
+    <description>
+      Tools for helping debug Lon-CAPA
+    </description>
+<filenames>
+activity_to_accesscount.pl;
+clean_db.pl;
+dump_db.pl;
+escape.pl;
+excise_from_db.pl;
+getties.pl;
+login_count.pl;
+modify_config_files.pl;
+parse_scantron.pl;
+seed_accesscount.pl;
+stress.pl;
+unescape.pl;
+user_login_count.pl;
+</filenames>
+</fileglob>
+<file>
+<source>loncom/build/distprobe</source>
+<target dist='default'>home/httpd/perl/distprobe</target>
+<categoryname>script</categoryname>
+<description>
+for probing operating system flavor and version
+</description>
+<note>
+</note>
+</file>
 </files>
 </lpml>