update documentation to match new directory structure

doc/0-Introduction.txt

@@ -27,6 +27,6 @@ Specifically:
  - The PTS documentation is available online in html format at
    <a href="http://www.skirt.ugent.be/pts">www.skirt.ugent.be/pts</a>.
  - Both can be downloaded as a PDF file from
-   <a href="http://www.skirt.ugent.be/downloads">www.skirt.ugent.be/downloads</a>.
+   <a href="http://www.skirt.ugent.be/downloads.html">www.skirt.ugent.be/downloads</a>.
 
 */

doc/1-InstallationGuide.txt

@@ -46,16 +46,15 @@ PTS has been developed and tested with the academic edition of the Enthought Pyt
 of the full EPD fortunately is available to academic institutions at no cost. It includes a large number of scientific
 packages, and it is offered as a one-click installer for various platforms.
 
-Go to the <a href="http://www.enthought.com/products/getepd.php">Enthought download page</a>
+Go to the <a href="https://www.enthought.com/store">Enthought download page</a>
 and click on the "ACADEMIC" button at the bottom of the page. After entering your academic email address
-you will receive a message with the download link. Download the most recent version of the installers:
+you will receive a message with the download link. Download the installers:
 PTS was tested with \c epd-7.3-1-macosx-i386.dmg on Mac OS X and \c epd-7.3-1-rh5-x86_64.sh on Ubuntu.
 Finally run the installer on your computer following the usual procedures.
 
 \subsection InstallPythonPacks Python packages used by PTS
 
-As you can see on the <a href="http://www.enthought.com/products/epdlibraries.php">Enthought package index page</a>,
-the EPD includes a lot of pre-installed Python packages. The table below offers a list of the subset actually
+The EPD includes a lot of pre-installed Python packages. The table below offers a list of the subset actually
 used by PTS at this time. Future version of PTS may rely on other packages, as long as they are included in the EPD.
 
 <TABLE>
@@ -74,9 +73,8 @@ used by PTS at this time. Future version of PTS may rely on other packages, as l
 <TR><TD>sqlite3</TD>        <TD>2.6.0/3.7.3</TD>    <TD>Basic SQL database interface</TD></TR>
 </TABLE>
 
-\note EPD -- and consequently PTS -- is built on Python version 2.7.3, which is the most recent and probably the
-last update of Python 2. It does not use Python 3 because some of the required packages are not yet available in
-this newer and slightly incompatible version of Python.
+\note EPD 7.3 -- and consequently PTS -- is built on Python version 2.7.3. It does not use Python 3 because
+some of the required packages are not yet available in this newer and slightly incompatible version of Python.
 
 
 \section InstallSource Installing the PTS source code
@@ -99,7 +97,7 @@ Now obtain the PTS source code from the GitHub repository as follows:
 
 \verbatim
 cd ~/PTS
-git clone git@github.ugent.be:pcamps/PTS.git git
+git clone git@github.ugent.be:SKIRT/PTS.git git
 \endverbatim
 
 To update the local copy of the source code after changes were made to the repository, use:
@@ -160,6 +158,6 @@ you can use Qt Creator to edit PTS source files.
 To enable syntax coloring for Python source code in the Qt Creator editor, choose the "Qt Creator->Preferences..."
 menu item to open the preferences panel. On the "Text Editor -> Generic Highlighter" tab, press the
 "Download Definitions..." button. In the new dialog, locate and select the "Python" item in the long list, and press
-the "Download Selected Definitions" buttons. Close the dialog and the preferences panel.
+the "Download Selected Definitions" button. Close the dialog and the preferences panel.
 
 */

doc/2-UsersGuide.txt

@@ -5,7 +5,6 @@
 \section UserIntro Introduction
 
 This chapter explains the overall philosophy behind PTS and provides overall usage guidelines.
-Since PTS is still under active development, things may change over time.
 
 \section UserPhil Philosophy behind PTS
 
@@ -50,19 +49,21 @@ The intention is to include the following types of functionality in PTS (the lis
 
 \subsection UserUseDirs PTS source code directories
 
-The PTS Python source code resides in two directories inside the \c PTS/svn/src directory:
+The PTS Python source code resides in three directories inside the \c PTS/git directory:
  - the \c pts directory contains the Python code for all toolkit classes and functions; i.e. the bulk of the PTS
    functionality. The files in this directory make up a Python \em package in the formal meaning of the word;
    each source file can be imported as a Python \em module.
+ - the \c eagle directory contains Python classes and functions dedicated to the EAGLE project;
+   see the \ref EagleGuide for more information.
  - the \c do directory contains a set of small Python scripts intended to be invoked from the command line.
    Strictly speaking these files are not part of a package since they cannot be imported as a module.
 
 An overview of the files in each directory, with links to a more detailed description, can be found in the
-reference material for "namespaces", a slightly unusual term automaatically generated by the documentation system.
+reference material for "namespaces", a slightly unusual term automatically generated by the documentation system.
 
 \subsection UserUsePts Using classes and functions in the pts directory
 
-The files in the \c PTS/svn/src/pts directory make up a Python \em package in the formal meaning of the word;
+The files in the \c pts directory make up a Python \em package in the formal meaning of the word;
 each source file can be imported as a \em module. For example, to obtain information on the instruments in a ski file
 called "mysim.ski" (residing in the current directory), you may enter the following commands in a Terminal window:
 
@@ -98,7 +99,7 @@ Please refer to the documentation for each individual module for more details on
 
 \subsection UserUseDo Using scripts in the do directory
 
-The Python scripts in the \c PTS/svn/src/do directory are intended to be invoked from the command line.
+The Python scripts in the \c do directory are intended to be invoked from the command line.
 Most scripts accept one or more command line arguments and call on functions in the Python Toolkit for SKIRT (PTS),
 effectively exposing PTS functionality to the command line.
 

doc/3-DevelopersGuide.txt

@@ -30,4 +30,56 @@ In addition the \c git directory contains subdirectories holding the source and
   - the \c do subdirectory contains a number of Python scripts that use the PTS facilities to perform concrete tasks;
   - the \c doc subdirectory contains text files with additional documentation that doesn't fit inside the source code.
 
+\section DevBuildDocs Building the documentation
+
+The PTS documentation is generated from the Python source files (and from the extra files in the \c doc directory)
+by Doxygen. For information on how to install this free application, refer to the section
+"Installing the documentation generator" in the SKIRT documentation.
+
+The \c git directory contains shell scripts for building and publishing the documentation. These scripts have been
+tested on Mac OS X only and will need to be adjusted for use on other systems. Before invoking
+the scripts for the first time, you may need to make them executable as follows:
+
+\verbatim
+cd ~/PTS/git
+chmod +rx makeHTML.sh
+chmod +rx makePDF.sh
+chmod +rx publishToWebHost.sh
+\endverbatim
+
+To build the HTML documentation, enter:
+
+\verbatim
+cd ~/PTS/git
+./makeHTML.sh
+\endverbatim
+
+The resulting HTML files are placed in the \c html directory next to (i.e. at the same level as) the \c git directory.
+As usual, the file \c index.html provides the starting point for browsing. In addition, Doxygen places a Qt help
+archive with the same contents in the \c doc directory next to the \c git directory (not to be confused with the
+\c doc directory \em inside the \c git directory).
+
+When you run the script for the first time, Doxygen creates the \c html directory and it contents from scratch.
+If you run the script again after you modified the source code (or the extra documentation files),
+Doxygen only processes the changes so it completes a lot faster.
+
+Similarly, to build the PDF documentation, enter:
+
+\verbatim
+cd ~/PTS/git
+./makePDF.sh
+\endverbatim
+
+The output PDF file is placed in the \c doc directory next to the \c git directory (not to be confused with the
+\c doc directory \em inside the \c git directory).
+
+Finally, to publish the documentation to the SKIRT web site, enter:
+
+\verbatim
+cd ~/PTS/git
+./publishToWebHost.sh
+\endverbatim
+
+The script will request the password that provides write access to the SKIRT web area.
+
 */