I am on windows and to better handle the situation, I create a consolidated d:\opengroksrc
folder which contains all my scattered source directories as directory junctions
Example I have a project in d:\gitsrc and another project in d:\hacksrc.
I have created a folder named d:\opengroksrc
d:\opengroksrc
'-gitsrc => hardlink to d:\gitsrc
'-hacksrc => hardlink to d:\hacksrc
mklink /j d:\opengroksrc\gitsrc d:\gitsrc
can be used to create a junction for a directory in windows
and in my web.xml
I indicate that my source are actually coming from d:\opengroksrc
<context-param>
<param-name>SRC_ROOT</param-name>
<param-value>D:\opengroksrc\</param-value>
</context-param>
And finally for indexing
java -jar E:\opengrok\lib\opengrok.jar -a on -t 4 -W E:\opengrok\configuration.xml -c C:\Windows\ctags.exe -P -S -v -s D:\opengroksrc -d E:\opengrok\grokdata -I *.cs -I *.c -I *.cpp -I *.h -I *.xml