--- doc/loncapafiles/loncapafiles.lpml	2003/06/16 15:14:29	1.251
+++ doc/loncapafiles/loncapafiles.lpml	2003/09/11 19:47:30	1.280
@@ -2,7 +2,7 @@
  "http://lpml.sourceforge.net/DTD/lpml.dtd">
 <!-- loncapafiles.lpml -->
 
-<!-- $Id: loncapafiles.lpml,v 1.251 2003/06/16 15:14:29 bowersj2 Exp $ -->
+<!-- $Id: loncapafiles.lpml,v 1.280 2003/09/11 19:47:30 www Exp $ -->
 
 <!--
 
@@ -459,6 +459,12 @@ extensions</description>
 </directory>
 <directory dist='default'>
   <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/jme</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>JME support files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/helper</targetdir>
   <categoryname>server readonly</categoryname>
   <description>XML specifications for helpers</description>
@@ -551,6 +557,13 @@ LON-CAPA system.</description>
 </directory>
 <directory dist='default'>
   <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/res/lib/templates</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Resource library
+  </description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/includes</targetdir>
   <categoryname>server readonly</categoryname>
   <description>files useful for including within customized scripting
@@ -625,7 +638,7 @@ are viewable over the world-wide web</de
   <protectionlevel>never_delete</protectionlevel>
   <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='redhat8'>usr/lib/perl5/site_perl/5.8.0</targetdir>
+  <targetdir dist='redhat8 redhat9'>usr/lib/perl5/site_perl/5.8.0</targetdir>
   <targetdir dist='debian'>usr/local/lib/perl/5.6.0</targetdir>
   <categoryname>standard</categoryname>
   <description>system perl tree (usually present on linux systems)
@@ -784,7 +797,7 @@ well as causing the Apache module to be
 <description>
 Thesaurus database file to be built from loncom/thesaurus/rawkey.txt
 </description>
-<build trigger='run if dependencies change'>
+<build trigger='always run'>
 loncom/thesaurus/build_thesaurus_wrapper.sh
 </build>
 <dependencies>
@@ -825,6 +838,22 @@ parameter.
 </description>
 </file>
 <file>
+<source>loncom/cgi/takeoffline.pl</source>
+<target dist='default'>home/httpd/cgi-bin/takeoffline.pl</target>
+<categoryname>script</categoryname>
+<description>
+Take machine offline
+</description>
+</file>
+<file>
+<source>loncom/cgi/takeonline.pl</source>
+<target dist='default'>home/httpd/cgi-bin/takeonline.pl</target>
+<categoryname>script</categoryname>
+<description>
+Take machine online
+</description>
+</file>
+<file>
 <source>loncom/cgi/thumbnail.gif</source>
 <target dist='default'>home/httpd/cgi-bin/thumbnail.gif</target>
 <categoryname>script</categoryname>
@@ -941,6 +970,38 @@ out all records in "|"-separated format.
 To be used by very simple harvesting engines.
 </description>
 </file>
+<file>
+<source>loncom/homework/simpleproblem.problem</source>
+<target dist='default'>home/httpd/html/res/lib/templates/simpleproblem.problem</target>
+<categoryname>interface file</categoryname>
+<description>
+Generic resource for DOCS "Simple Problem"
+</description>
+</file>
+<file>
+<source>loncom/homework/simpleproblem.problem.meta</source>
+<target dist='default'>home/httpd/html/res/lib/templates/simpleproblem.problem.meta</target>
+<categoryname>interface file</categoryname>
+<description>
+Meta file for generic resource for DOCS "Simple Problem"
+</description>
+</file>
+<file>
+<source>loncom/homework/templates/examupload.problem</source>
+<target dist='default'>home/httpd/html/res/lib/templates/examupload.problem</target>
+<categoryname>interface file</categoryname>
+<description>
+Generic resource for score upload
+</description>
+</file>
+<file>
+<source>loncom/homework/templates/examupload.problem.meta</source>
+<target dist='default'>home/httpd/html/res/lib/templates/examupload.problem.meta</target>
+<categoryname>interface file</categoryname>
+<description>
+Meta file for generic resource for score upload
+</description>
+</file>
 <fileglob>
 <glob>*.*</glob>
 <sourcedir>loncom/homework/templates/</sourcedir>
@@ -959,6 +1020,8 @@ ClickImageExample.problem;
 ClickImageExample.problem.meta;
 Essay.problem;
 Essay.problem.meta;
+examupload.problem;
+examupload.problem.meta;
 man1.jpg;
 numerical.problem;
 numerical.problem.meta;
@@ -1015,8 +1078,8 @@ Built from Glabel.java.  Still working o
 </note>
 </file>
 <file>
-<source>loncom/interface/default.assesscalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.assesscalc
+<source>loncom/interface/spreadsheet/default_assesscalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_assesscalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -1024,8 +1087,8 @@ Default spreadsheet for individual asses
 </description>
 </file>
 <file>
-<source>loncom/interface/default.studentcalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.studentcalc
+<source>loncom/interface/spreadsheet/default_studentcalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_studentcalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -1033,8 +1096,8 @@ Default spreadsheet for assessment of st
 </description>
 </file>
 <file>
-<source>loncom/interface/default.classcalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.classcalc
+<source>loncom/interface/spreadsheet/default_classcalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_classcalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -1099,7 +1162,7 @@ in <tt>access.conf</tt>
 <file>
 <source>loncom/htpasswd</source>
 <target dist='default'>home/httpd/lonTabs/htpasswd</target>
-<categoryname>conf</categoryname>
+<categoryname>static conf</categoryname>
 <description>
 Basic auth password to access /lon-status and /server-status
 </description>
@@ -1424,6 +1487,15 @@ Interface file for responding to imprope
 </description>
 </file>
 <file>
+<source>loncom/html/adm/notinit.html</source>
+<target dist='default'>home/httpd/html/adm/notinit.html</target>
+<categoryname>interface file</categoryname>
+<description>
+Interface file for responding to accessing uploaded resources without
+re-initializing course.
+</description>
+</file>
+<file>
 <source>loncom/html/adm/overloaded.txt</source>
 <target dist='default'>home/httpd/html/adm/overloaded.txt</target>
 <categoryname>interface file</categoryname>
@@ -1564,6 +1636,15 @@ Handler to put up syllabus
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/homework/lonsimpleproblemedit.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonsimpleproblemedit.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to set parameters for simple homework problems
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/lonsimplepage.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonsimplepage.pm</target>
 <categoryname>handler</categoryname>
@@ -1837,9 +1918,13 @@ Tex files for the help system
 </description>
 <filenames>
 About_Authors_Manual.tex;
+About_Communication.tex;
+About_Developers_Manual.tex;
 About_Numerical_and_Formula_Response.tex;
 Ambiguous_Reference.tex;
 Analyze_Problem.tex;
+Annotation.tex;
+Authentication.tex;
 Author_LON-CAPA_Introduction.tex;
 Author_Manual_Title_Page.tex;
 Author_Numerical_and_Formula.tex;
@@ -1858,6 +1943,7 @@ Authoring_M_Tag.tex;
 Authoring_NumericalResponse.tex;
 Authoring_OptionResponse.tex;
 Authoring_Output_Tags.tex;
+Authoring_Pictures_EPS.tex;
 Authoring_Piecewise_Plot.tex;
 Authoring_RadiobuttonResponse.tex;
 Authoring_Response_Attributes.tex;
@@ -1866,17 +1952,28 @@ Authoring_Responseparam_Parameter.tex;
 Authoring_Scripting_Tags.tex;
 Authoring_Structure_Tags.tex;
 Authoring_XML_Intro.tex;
+Bookmarks.tex;
+Bugzilla.tex;
 CAPA_LON-CAPA_function_diffs.tex;
+Caching.tex;
 Calendar_Add_Announcement.tex;
 Calendar_Remove_Announcement.tex;
 Calling_Functions.tex;
+Cascading_Parameters.tex;
+Change_Colors.tex;
+Change_Password.tex;
 Chart_Description.tex;
 Chart_Output_Data.tex;
 Chart_Output_Formats.tex;
+Chatting.tex;
 Coauthor.tex;
 Construction_Space_Overview.tex;
+Course_Add_Other.tex;
 Course_Add_Student.tex;
+Course_Broadcast_Message.tex;
+Course_Change_Privileges.tex;
 Course_Chart_To_Excel.tex;
+Course_Chat.tex;
 Course_Convert_To_CSV.tex;
 Course_Create_Class_List.tex;
 Course_Critical_Message.tex;
@@ -1885,30 +1982,53 @@ Course_Disable_Discussion.tex;
 Course_Discussion_Board.tex;
 Course_Drop_Student.tex;
 Course_Edit_Content.tex;
+Course_Editing_Custom_Roles.tex;
+Course_Extending_Due_Dates.tex;
+Course_Face_To_Face_Records.tex;
 Course_Feedback_Addresses.tex;
 Course_Homework_Performance_Overview.tex;
 Course_Manual_Title_Page.tex;
+Course_Manually_Grade_Problem.tex;
+Course_Maximum_Collaborators.tex;
 Course_Message_Access.tex;
+Course_Modify_Student_Data.tex;
+Course_Parameter_Levels.tex;
 Course_Problem_Weight.tex;
+Course_Set_Start_End_Date.tex;
 Course_Setting_Parameters.tex;
 Course_Student_Grade_Override.tex;
 Course_Student_Work.tex;
 Course_Toplevel_Seq.tex;
+Course_User_Evaluation.tex;
+Course_User_Parameter.tex;
+Course_View_Class_List.tex;
 Create_Course.tex;
 Creating_A_Course_Intro.tex;
 Creating_New_Content_Pages.tex;
 Creating_Online_Problems.tex;
 Creating_Radio_Response_Problems.tex;
+Developer_Manual_Title_Page.tex;
+Developer_Tutorial.tex;
+Docs_About_Bulletin_Board.tex;
+Docs_About_My_Personal_Info.tex;
+Docs_About_Simple_Page.tex;
+Docs_About_Syllabus.tex;
 Docs_Adding_Course_Doc.tex;
 Docs_Adding_External_Resource.tex;
 Docs_Adding_Folders.tex;
+Docs_Adding_Syllabus.tex;
+Docs_Alternatives.tex;
 Docs_Creating_From_Template.tex;
+Docs_Editing_Templated_Pages.tex;
 Docs_Importing_LON-CAPA_Resource.tex;
+Docs_Load_Map.tex;
 Docs_Main_Course_Documents.tex;
 Docs_Navigate_Content.tex;
 Docs_Overview.tex;
+Docs_Score_Upload_Form.tex;
 Docs_Supplemental.tex;
 Docs_Uploading_From_Harddrive.tex;
+Finding_Resources.tex;
 Foils.tex;
 Formula_Response_Adv_Intro.tex;
 Formula_Response_Example.tex;
@@ -1918,9 +2038,18 @@ Formula_Response_Sampling.tex;
 Formula_Tolerance.tex;
 General_Intro.tex;
 Greek_Symbols.tex;
+Guts_Apache.tex;
+Guts_Apache_Env.tex;
+Guts_Apache_Modules.tex;
+Guts_Authentication.tex;
+Guts_Authoring.tex;
+Guts_Coding_Guidelines.tex;
+Guts_Course_Dir.tex;
+Guts_User_Dir.tex;
 How_To_Edit_Existing_Content_Pages.tex;
 Latex_Footer.tex;
 Latex_Header.tex;
+Leaving_Feedback.tex;
 Login_To_LON-CAPA.tex;
 Metadata_Description.tex;
 Navmap_Host_Down.tex;
@@ -1944,7 +2073,11 @@ Option_Response_Problems.tex;
 Option_Response_Simple.tex;
 Other_Symbols.tex;
 Part_Tag_Edit_Help.tex;
+Personal_Info_Page.tex;
 Physical_Units.tex;
+Prefs_Forwarding.tex;
+Prefs_Screen_Name_Nickname.tex;
+Print_Resource.tex;
 Problem_Editor_Testing_Area.tex;
 Problem_Editor_XML_Index.tex;
 Problem_LON-CAPA_Functions.tex;
@@ -1958,11 +2091,15 @@ Quick_Grades_Possibly_Correct.tex;
 Radio_Response_Problems.tex;
 Radio_Response_Randomization.tex;
 Ranking_Problems.tex;
+Receipt.tex;
+Resource_Discussion.tex;
 Resource_Types.tex;
+Roles_About.tex;
 Script_Functions.tex;
 Script_Tutorial_Intro.tex;
 Script_Variables.tex;
 Scripting_Help.tex;
+Sending_Email.tex;
 Sequence_Advanced_Editor_Creation.tex;
 Sequence_Definition.tex;
 Sequence_Editor_Selection.tex;
@@ -1971,25 +2108,26 @@ 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_Calculation.tex;
+Spreadsheet_Calculation_Time.tex;
+Spreadsheet_Cell_Editing.tex;
+Spreadsheet_Editing.tex;
 Spreadsheet_Export_Row.tex;
+Spreadsheet_Files.tex;
 Spreadsheet_Functions.tex;
-Spreadsheet_Import_Values.tex;
+Spreadsheet_Hierarchy.tex;
+Spreadsheet_HowTo_Assessments.tex;
+Spreadsheet_HowTo.tex;
+Spreadsheet_Layout.tex;
 Spreadsheet_Levels.tex;
-Spreadsheet_Lists.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_Referencing_Cells.tex;
+Spreadsheet_Referencing_Parameters.tex;
+Spreadsheet_Row_Numbers.tex;
+Spreadsheet_Student_View.tex;
 Spreadsheet_Student_Visible.tex;
-Spreadsheet_Symbolic_Names.tex;
 Spreadsheet_Template_Row.tex;
 Spreadsheet_Ternary_Operator.tex;
 Spreadsheet_Tries.tex;
@@ -2005,6 +2143,8 @@ Variable_Tutorial_A.tex;
 Variables_in_Scripts.tex;
 Variables_in_the_Answer_Block.tex;
 Variables_in_the_Text_Block.tex;
+What_Is_LON-CAPA.tex;
+Why_LON-CAPA.tex;
 all_functions_table.tex;
 </filenames>
 </fileglob>
@@ -2417,6 +2557,33 @@ assignment.
 </description>
 <status>works/unverified</status>
 </file>
+
+<file>
+  <source>loncom/homework/chemresponse.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/chemresponse.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+    Handle the tags organicresponse/structure and reationresponse
+  </description>
+  <status>works/unverified</status>
+</file>
+
+<fileglob>
+  <glob>*.*</glob>
+  <sourcedir>loncom/html/adm/jme/</sourcedir>
+  <targetdir dist='default'>home/httpd/html/adm/jme/</targetdir>
+  <categoryname>interface file</categoryname>
+  <description>
+    JME files, for editing organic structures
+  </description>
+  <filenames>
+JME.jar;
+jme.gif;
+jme_help.html;
+nitro.gif;
+smiles.gif
+  </filenames>
+</fileglob>
 <file>
 <source>loncom/interface/lontest.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lontest.pm</target>
@@ -3481,6 +3648,12 @@ loncom/build/pod2html.sh ../lonnet/perl/
 <description>bumps to login</description>
 </file>
 <file>
+<source>loncom/html/index.html</source>
+<target dist='default'>home/httpd/html/origindex.html</target>
+<categoryname>interface file</categoryname>
+<description>bumps to login, backup for takeonline</description>
+</file>
+<file>
 <source>loncom/html/favicon.ico</source>
 <target dist='default'>home/httpd/html/favicon.ico</target>
 <categoryname>interface file</categoryname>
@@ -3780,6 +3953,7 @@ jar_big.gif;
 jpg.gif;
 jpg_big.gif;
 latex.gif;
+library.gif;
 lipsrsealed.gif;
 lite.gif;
 liteani.gif;
@@ -3897,7 +4071,7 @@ subm_button.gif
 <source>loncom/xml/tth.pm</source>
 <target dist='default'>usr/lib/perl5/site_perl/5.005/tth.pm</target>
 <target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/tth.pm</target>
-<target dist='redhat8'>home/httpd/lib/perl/tth.pm</target>
+<target dist='redhat8 redhat9'>home/httpd/lib/perl/tth.pm</target>
 <categoryname>system file</categoryname>
 <description>
 perl module for invoking functions specific to TeX-to-HTML conversion
@@ -3931,6 +4105,15 @@ tested
   <status>works/verified</status>
 </file>
 <file>
+  <source>loncom/LondTransaction.pm</source>
+  <target dist='default'>home/httpd/lib/perl/LONCAPA/LondTransaction.pm</target>
+  <categoryname>system file</categoryname>
+  <description>
+	Handles a single lon-capa insternal transaction
+  </description>
+  <status>works/verified</status>
+</file>
+<file>
    <source>loncom/types/HashIterator.pm</source>
    <target dist='default'>home/httpd/lib/perl/LONCAPA/HashIterator.pm</target>
    <categoryname>system file</categoryname>
@@ -3982,7 +4165,7 @@ entries.
 <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>
-<target dist='redhat8'>home/httpd/lib/perl/tth.so</target>
+<target dist='redhat8 redhat9'>home/httpd/lib/perl/tth.so</target>
 <categoryname>system file</categoryname>
 <description>
 shared library file for dynamic loading and unloading
@@ -4006,7 +4189,7 @@ modules/TexConvert/tthperl/commands
 <source>loncom/homework/caparesponse/capa.pm</source>
 <target dist='default'>usr/lib/perl5/site_perl/5.005/capa.pm</target>
 <target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.pm</target>
-<target dist='redhat8'>home/httpd/lib/perl/capa.pm</target>
+<target dist='redhat8 redhat9'>home/httpd/lib/perl/capa.pm</target>
 <categoryname>system file</categoryname>
 <description>
 perl module for invoking functions specific to CAPA
@@ -4022,7 +4205,7 @@ the build process however.
 <source>loncom/homework/caparesponse/capa.bs</source>
 <target dist='default'>usr/lib/perl5/site_perl/5.005/capa.bs</target>
 <target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.bs</target>
-<target dist='redhat8'>home/httpd/lib/perl/capa.bs</target>
+<target dist='redhat8 redhat9'>home/httpd/lib/perl/capa.bs</target>
 <categoryname>system file</categoryname>
 <description>
 bootstrap file associated with dynamic loading of this module on multiple
@@ -4039,7 +4222,7 @@ the build process however.
 <source>loncom/homework/caparesponse/capa.so</source>
 <target dist='default'>usr/lib/perl5/site_perl/5.005/capa.so</target>
 <target dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0/capa.so</target>
-<target dist='redhat8'>home/httpd/lib/perl/capa.so</target>
+<target dist='redhat8 redhat9'>home/httpd/lib/perl/capa.so</target>
 <categoryname>system file</categoryname>
 <description>
 shared library file for dynamic loading and unloading
@@ -4230,7 +4413,11 @@ sunysb.gif;
 udel.gif;
 uz.gif;
 fvl.gif;
+csm.gif;
+fit.gif;
+nau.gif;
 glps.gif;
+BCHS.gif;
 headersfu.gif;
 uwsp.gif
 </filenames>
@@ -4245,6 +4432,10 @@ uwsp.gif
 annarbor.tab;
 default.tab;
 msu.tab;
+csm.tab;
+fit.tab;
+nau.tab;
+fsu.tab;
 sfu.tab;
 worf.tab
 </filenames>