Change documentation URLs to GitHub for now until Jenkins is updated.

README.md

@@ -53,17 +53,14 @@ specified in the file LICENSE.
 Documentation
 =============
   The `/doc` subdirectory contains PDF and LyX versions of the CPPTRAJ manual.
-The latest version of the manual is compiled each time new code is merged
-and is available for download
-[here.](https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/lastSuccessfulBuild/artifact/doc/CpptrajManual.pdf)
+The latest version of the manual is available for download
+[here.](https://raw.githubusercontent.com/Amber-MD/cpptraj/master/doc/CpptrajManual.pdf)
 An HTML version can be found [here](https://amber-md.github.io/cpptraj/). There
 is also limited help for commands in interactive mode via `help [<command>]`;
 `help` with no arguments lists all known commands.
 
-  Code documentation generated by doxygen are available
-[here.](https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/PR-773/Doxygen_20Documentation/)
-You can generate the documentation yourself with the command `make docs`. A
-limited developers guide is available [here](https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/lastSuccessfulBuild/artifact/doc/CpptrajDevelopmentGuide.pdf)
+  Code documentation generated by Doxygen can be generated with the command `make docs`. A
+limited developers guide is available [here](https://raw.githubusercontent.com/Amber-MD/cpptraj/master/doc/CpptrajDevelopmentGuide.pdf)
 and limited HTML-formatted documentation is available
 [here](https://amber-md.github.io/cpptraj/).