thanks to some other posts on here as well as the 
guide from Tom, I was able to get comskip running on my new linux install of Sage. However, there are two things that I just can't seem to get right.
1) It will only run with the plugin-supplied version of comskip. Whenever I try to set it to run with the donator version, comskip won't run. I have a "comskipd" directory with the donator files, and it appears to me to be setup identically to the "comskip" directory. There is no error that I can find, comskip just doesn't fire.
	Code:
	drwxr-xr-x  2 root root     4096 May 30  2011 comskip
drwxr-xr-x  2 root root     4096 Aug 23 10:26 comskipd
comskip:
total 1792
drwxr-xr-x  2 root root   4096 May 30  2011 .
drwxr-xr-x 21 root root  20480 Aug 23 13:00 ..
-rw-r--r--  1 root root   1535 Nov 25  2004 comskip.dictionary
-rw-r--r--  1 root root 724992 Mar 14  2011 comskip.exe
-rw-r--r--  1 root root 724992 Mar 14  2011 comskipGUI.exe
-rw-r--r--  1 root root   6022 May 30  2011 comskip.ini
-rw-r--r--  1 root root    466 May 30  2011 comskip.ini changes for CommercialDetector.txt
-rw-r--r--  1 root root  22973 Feb 17  2011 comskip.txt
-rw-r--r--  1 root root  26758 Feb 23  2006 debugwindow.htm
-rw-r--r--  1 root root  16384 Apr 27  2006 HideRun.exe
-rw-r--r--  1 root root  55813 Mar 31  2006 manual.htm
-rw-r--r--  1 root root   2230 Apr  1  2006 PostProcessing.bat
-rw-r--r--  1 root root  50021 Mar 14  2011 readme.txt
-rw-r--r--  1 root root 157774 Oct 27  2006 tuning.htm
comskipd:
total 24428
drwxr-xr-x  2 root root    4096 Aug 23 10:26 .
drwxr-xr-x 21 root root   20480 Aug 23 13:00 ..
-rw-r--r--  1 root root 6781433 Jul 17 10:21 comskip81_056_donators.zip
-rw-r--r--  1 root root    1535 Nov 25  2004 comskip.dictionary
-rw-r--r--  1 root root 8918698 Jul 17 16:18 comskip.exe
-rw-r--r--  1 root root 8918698 Jul 17 16:18 comskipGUI.exe
-rw-r--r--  1 root root    6132 Aug 23 11:57 comskip.ini
-rw-r--r--  1 root root   23768 Dec 30  2012 comskip.txt
-rw-r--r--  1 root root   26758 Feb 23  2006 debugwindow.html
-rw-r--r--  1 root root   16384 Apr 27  2006 HideRun.exe
-rw-r--r--  1 root root   55813 Mar 31  2006 manual.html
-rw-r--r--  1 root root    2230 Apr  1  2006 PostProcessing.bat
-rw-r--r--  1 root root   59793 Jul 17 16:19 readme.txt
-rw-r--r--  1 root root  157774 Oct 27  2006 tuning.html
 This isn't a huge deal to me since I don't have any H.264 files to scan, but I would like to be able to edit the comskip.ini file, but i don't think I can do that if I'm not supposed to edit the plugin supplied one.
2) I have 200 shows that haven't been scanned for commercials. When i drill into the plugin configuration, I get a Java null.pointer error when i try to ask the comskip plugin to go to work on these 200 shows. (if i knew how to script or otherwise automate scanning these shows from the command line, i'd be fine with that. i just don't want to run comskip on each of them from the command line individually - especially since it isn't easy to identify which files have and haven't been scanned.)
See error attached.
thanks!
Matt