Thanks for doing this. I had an installation from a couple of years ago that was a much bigger pain, so this is great to have.
I had one small problem during installation that I wanted to report just in case anyone else has the same issue. I've seen it mentioned in passing here and there but not set down in one place. So I hope this is helpful to someone.
I'm doing a brand new install to a clean directory, using the GOG installer. I'm running Windows 7. I accepted the default directory name "Freespace 2" but placed it in "D:\games\flightsims\Freespace 2". Everything but the GOG installer worked OK, but that part logged an InnoExtract error:
2014-07-02 21:13:47,260 [pool-1-thread-1] INFO com.fsoinstaller.utils.MiscUtils - Command to run: innoextract.exe --quiet --list E:\installers\games\GoG\freespace_2\setup_freespace2_2.0.0.8.exe
2014-07-02 21:13:47,461 [pool-1-thread-1] INFO com.fsoinstaller.wizard.InnoExtractTask - ...done
2014-07-02 21:13:47,462 [pool-1-thread-1] INFO com.fsoinstaller.wizard.InnoExtractTask - Extracting 243 files...
2014-07-02 21:13:47,462 [pool-1-thread-1] DEBUG com.fsoinstaller.utils.MiscUtils - Detected Windows; using CMD.EXE...
2014-07-02 21:13:47,462 [pool-1-thread-1] INFO com.fsoinstaller.utils.MiscUtils - Command to run: innoextract.exe --quiet --output-dir "D:\games\flightsims\Freespace 2\7b0eab4643ad460b8307e8e23f5173ac" E:\installers\games\GoG\freespace_2\setup_freespace2_2.0.0.8.exe
[... trimmed the innoextract usage message, in both DEBUG and ERROR level logs ...]
2014-07-02 21:13:47,536 [pool-1-thread-1] ERROR com.fsoinstaller.wizard.InnoExtractTask - stderr: Error parsing command-line: the argument ('D:\games\flightsims\Freespace 2\7b0eab4643ad460b8307e8e23f5173ac') for option '--dir' is invalid
2014-07-02 21:13:47,536 [pool-1-thread-1] ERROR com.fsoinstaller.wizard.InnoExtractTask - stderr:
2014-07-02 21:13:47,536 [pool-1-thread-1] ERROR com.fsoinstaller.wizard.InnoExtractTask - Could not extract files using innoextract!
java.io.IOException: InnoExtract reported exit code 1
at com.fsoinstaller.wizard.InnoExtractTask.runProcess(InnoExtractTask.java:215)
On a hunch I renamed my install directory to 'Freespace2' and tried again, and that worked fine. I'd think it would have been fine because of the quotes around the path, but I'm a Unix guy and not an expert on the windows shell. My setup must be unusual (maybe the extra path element?). I didn't test with an equally long path but no space, so maybe it's a length issue not a space issue; the install path is 32 characters without the hex junk and 64 with it, and things going wrong around powers of 2 make me nervous.
(watch, not the very next thread I read is going to be a huge blinking warning about this I somehow missed before.

)