--- doc/loncapafiles/loncapafiles.lpml	2002/04/27 21:35:25	1.121
+++ doc/loncapafiles/loncapafiles.lpml	2002/08/07 15:55:40	1.156
@@ -3,7 +3,7 @@
 <!-- loncapafiles.lpml -->
 <!-- Scott Harrison -->
 
-<!-- $Id: loncapafiles.lpml,v 1.121 2002/04/27 21:35:25 harris41 Exp $ -->
+<!-- $Id: loncapafiles.lpml,v 1.156 2002/08/07 15:55:40 albertel Exp $ -->
 
 <!--
 
@@ -216,7 +216,7 @@ echo '**********************************
 <rpmRequires>
 <item>PreReq: LON-CAPA-setup</item>
 <item>PreReq: apache</item>
-<item>PreReq: /etc/httpd/conf/access.conf</item>
+<item>PreReq: /etc/httpd/conf/httpd.conf</item>
 </rpmRequires>
 </rpm>
 <directories>
@@ -226,11 +226,6 @@ echo '**********************************
   <description>standard linux directory for configuration files</description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='default'>etc/atalk</targetdir>
-  <categoryname>standard</categoryname>
-  <description>appletalk configuration files</description>
-</directory>
-<directory dist='default'>
   <targetdir dist='default'>etc/cron.d</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for running time-based "jobs"
@@ -253,56 +248,50 @@ echo '**********************************
   </description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='redhat7 redhat7.1'>etc/samba</targetdir>
-  <categoryname>standard</categoryname>
-  <description>configuration directory for samba authentication
-  </description>
-</directory>
-<directory dist='default'>
   <targetdir dist='default'>etc/rc.d/init.d</targetdir>
-  <targetdir dist='debian2.2'>etc/init.d</targetdir>
+  <targetdir dist='debian'>etc/init.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run during system startup</description>
 </directory>
 <directory dist='default'>
   <targetdir dist='default'>etc/rc.d/rc0.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc0.d</targetdir>
+  <targetdir dist='debian'>etc/rc0.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 0</description>
 </directory>
 <directory dist='default'>
   <targetdir dist='default'>etc/rc.d/rc1.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc1.d</targetdir>
+  <targetdir dist='debian'>etc/rc1.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 1</description>
 </directory>
 <directory dist='default'>
   <targetdir dist='default'>etc/rc.d/rc2.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc2.d</targetdir>
+  <targetdir dist='debian'>etc/rc2.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 2</description>
 </directory>
 <directory dist='default'>
   <targetdir dist='default'>etc/rc.d/rc3.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc3.d</targetdir>
+  <targetdir dist='debian'>etc/rc3.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 3</description>
 </directory>
 <directory dist='default'>
   <targetdir dist='default'>etc/rc.d/rc4.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc4.d</targetdir>
+  <targetdir dist='debian'>etc/rc4.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 4</description>
 </directory>
 <directory dist='default'>
   <targetdir dist='default'>etc/rc.d/rc5.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc5.d</targetdir>
+  <targetdir dist='debian'>etc/rc5.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 5</description>
 </directory>
 <directory dist='default'>
   <targetdir dist='default'>etc/rc.d/rc6.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc6.d</targetdir>
+  <targetdir dist='debian'>etc/rc6.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 6</description>
 </directory>
@@ -348,6 +337,12 @@ Used by lond parent to check if children
   </description>
 </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>
@@ -364,6 +359,12 @@ Used by lond parent to check if children
   </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>
@@ -394,6 +395,11 @@ Used by lond parent to check if children
   <description>root of resource tree</description>
 </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>
@@ -409,6 +415,26 @@ Used by lond parent to check if children
   <description>online help documentation</description>
 </directory>
 <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
@@ -477,7 +503,8 @@ LON-CAPA system.</description>
 <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 dist='default'>
   <targetdir dist='default'>home/httpd/html/res/adm/pages</targetdir>
@@ -505,15 +532,26 @@ LON-CAPA system.</description>
 <directory dist='default'>
   <targetdir dist='default'>usr/lib/perl5/site_perl/5.005</targetdir>
   <targetdir dist='redhat7 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='debian'>usr/local/lib/perl/5.6.0</targetdir>
   <categoryname>standard</categoryname>
   <description>system perl tree (usually present on linux systems)
   </description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='default'>usr/local/bin</targetdir>
+  <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 binary files</description>
+  <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>
@@ -565,25 +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>
@@ -605,6 +641,25 @@ MySQL database</td></tr>
 </note>
 </file>
 <file>
+<source>loncom/loncapa_apache.conf</source>
+<target dist='default'>etc/httpd/conf/loncapa_apache.conf</target>
+<categoryname>static conf</categoryname>
+<description>
+The goal of this file is to implement all LON-CAPA specific
+customization of the Apache web server that does not require
+user input.
+
+For the Apache web server, it defines a global
+access configuration which defines what server options (Indexes", "Includes",
+"FollowSymLinks", "ExecCGI", or "MultiViews") are associated
+with specific directories ("/", "/home/httpd/html", "/home/httpd/cgi-bin",
+and "/usr/doc").  For the LON-CAPA network server and perl module
+handlers, it defines 
+and internal machine settings for specific directories, socket ports,
+the www@localhost MySQL password, and browser detection logic.
+</description>
+</file>
+<file>
 <source>loncom/startup.pl</source>
 <target dist='default'>etc/httpd/conf/startup.pl</target>
 <categoryname>static conf</categoryname>
@@ -616,13 +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>
@@ -641,6 +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>
@@ -650,6 +718,14 @@ 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>
@@ -738,12 +814,16 @@ blank.library;
 blank.library.meta;
 blank.problem;
 blank.problem.meta;
-formula.problem;
-formula.problem.meta;
+Essay.problem;
+Essay.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;
@@ -758,8 +838,8 @@ 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>
@@ -868,8 +948,7 @@ Basic auth password to access /lon-statu
 </file>
 <file>
 <source>loncom/smb.conf</source>
-<target dist='default'>etc/smb.conf</target>
-<target dist='redhat7 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
@@ -903,6 +982,14 @@ 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>
@@ -1060,6 +1147,17 @@ 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>
@@ -1140,7 +1238,7 @@ The relevant conditions and metadata to
 </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>
@@ -1194,6 +1292,33 @@ 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>
@@ -1204,6 +1329,264 @@ 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>
@@ -1213,6 +1596,33 @@ 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>
@@ -1283,7 +1693,8 @@ 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>
@@ -1458,11 +1869,19 @@ 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>
@@ -1643,6 +2062,15 @@ 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>
@@ -1916,7 +2344,7 @@ 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>
@@ -1956,7 +2384,7 @@ echo 'pod2html lonuserstate.pm'
 <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>
@@ -2151,6 +2579,34 @@ 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>
@@ -2619,7 +3075,7 @@ 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;
@@ -2738,9 +3194,7 @@ 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;
@@ -2781,6 +3235,17 @@ tested
 <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 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/tth.so</target>
@@ -2855,7 +3320,6 @@ commands;
 ../../../CAPA/pProj/capaGrammarDef.y;
 ../../../CAPA/pProj/capaFormula.y;
 ../../../CAPA/pProj/capaLexerDef.flex;
-../../../CAPA/pProj/capaToken.h;
 ../../../CAPA/pProj/capaFunction.c;
 ../../../CAPA/pProj/capaParserUtils.c;
 ../../../CAPA/pProj/capaMapExpr.c;
@@ -2867,8 +3331,14 @@ commands;
 ../../../CAPA/pProj/capaSubjective.c;
 ../../../CAPA/pProj/capaRQO.c;
 ../../../CAPA/pProj/capaFormulaLexer.c;
-../../../CAPA/pProj/capaFormulaParser.c;
-../../../CAPA/pProj/capaCommon.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>
@@ -2967,10 +3437,22 @@ Define unit prefixing and conversion for
 <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;
@@ -2978,12 +3460,14 @@ 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;
@@ -3015,6 +3499,7 @@ mrk.gif;
 n.gif;
 nav.gif;
 next.gif;
+nothumb.gif;
 o.gif;
 p.gif;
 parm.gif;
@@ -3032,6 +3517,7 @@ res.gif;
 roles.gif;
 s.gif;
 sbkm.gif;
+slash.gif;
 space.gif;
 spacer.gif;
 sprs.gif;
@@ -3080,7 +3566,7 @@ renders the HTML (including image maps)
 </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;
@@ -3181,7 +3667,7 @@ world2.gif
 </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;
@@ -3216,7 +3702,7 @@ ur_corner.gif
 </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;
@@ -3235,7 +3721,7 @@ javascript for handling client-side inte
 </file>
 <file>
 <source>loncom/build/check-rpms</source>
-<target dist='default'>usr/local/bin/check-rpms</target>
+<target dist='default'>usr/local/loncapa/bin/check-rpms</target>
 <categoryname>root script</categoryname>
 <description>
 compare installed rpms with up-to-date distribution
@@ -3342,7 +3828,7 @@ 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