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I don't know if anybody's already encountered this, but I ran into a few problems when trying to use FRED and FRED2, so I thought I should make a note about it here in case anybody else runs into them.
When following the walkthrough in the data/freddocs folder, when it comes time to save your mission, it says you should not change the directory but doesn't mention what that directory should be. Mine was defaulted at My Documents, but it really should be data/missions. I think this might be because FRED couldn't find the proper directory because it was installed into a GoG.com folder rather than its normal path, I'm not sure though.
The other issue seems to just be a weird bug in FRED itself. If you try to go to File > Run FreeSpace like the walkthrough tells you to, you'll get an error message saying "The system cannot find the file specified." For whatever reason, it looks like you have to rename FRED2 as FS2, and then that feature will work (but it isn't necessary as you can just run the normal FS2 client and access your custom mission anyway.)
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JonTron: I don't know if anybody's already encountered this, but I ran into a few problems when trying to use FRED and FRED2, so I thought I should make a note about it here in case anybody else runs into them.
When following the walkthrough in the data/freddocs folder, when it comes time to save your mission, it says you should not change the directory but doesn't mention what that directory should be. Mine was defaulted at My Documents, but it really should be data/missions. I think this might be because FRED couldn't find the proper directory because it was installed into a GoG.com folder rather than its normal path, I'm not sure though.
The other issue seems to just be a weird bug in FRED itself. If you try to go to File > Run FreeSpace like the walkthrough tells you to, you'll get an error message saying "The system cannot find the file specified." For whatever reason, it looks like you have to rename FRED2 as FS2, and then that feature will work (but it isn't necessary as you can just run the normal FS2 client and access your custom mission anyway.)

Hey thanks for your post. I have the same issues as you, and I am trying your fix(es) now. Thanks.
If you're into FRED-ing missions, you might consider upgrading to SPC.
The Source Code Project created some awsome SEXP and scripting possibilies and they ironed out some of the persistent bugs in the old engine.
Some of the things that are only possible with SCP:
-Multiple Docking
-Cinematic Missions with a Camera
-"Jump to Hyperspace" Effects
-Persistent Variables (These allow you to carry over stats from one mission to another).