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Came here looking for these and couldn't find them. Reposting in case anyone else was in the same boat.
NB. GOG Version 2.0 patch updates the game to version 1.03.1.
2.0 is the internal GOG version number, not the developer's number.

FTL Version 1.03.1

-Colorblind mode (available in options) makes many color pallette changes and adds additional symbols to help out our colorblind players.
I apologize for the delay in getting this into the game!
-Hotkeys added for many actions in the game, customizable from within the Options menu
-Indicator for when the enemy is attempting to jump away (and if it's able to)
-Cloaking will automatically cooldown in non-danger situations
-You can now pause using the middle mouse button
-Orange room borders for very low O2 have been replaced with hazard stripes on the floor
-Ctrl+click (customizable in Options) when aiming will allow you to specify a single weapon to auto-fire (or not auto-fire if auto-fire button is toggled)
-Minor balance change: System Repair drones power requirement reduced to 1

Major Bugs:
-Cloaking will provide the +60 evasion even if you don't have a pilot
-Beams will correctly damage crew (and start fires if the Fire Beam)
-Odd numbered Shield Systems will now properly repower after ionization
-Tough Little Ship, Astronomically Low Odds, and all of the Crystal Cruiser achievements fixed
-Repair/Anti-Personel Drones will always properly disappear whenever unequipped (or sold) - this will let you unequip them to make room for repair men if you system is destroyed
-Potential fix for rare crash when selecting weapons

Minor Bugs:
-Fixed: Zoltan Bonus power wouldn't update while paused for drones
-Federation Cruiser Artillery cooldown imagery properly updates during pause
-Fixed: Sometimes incorrectly displays the teleporter/shuttle text when your crew dies after battle
-All enemies (including boarders) will now have names
-Tooltips will properly clear when events/sub-windows open
-System limits/effects caused by events (or nebulas) update upon arrival, not after the event
-Cloaking system glow fixed
-Zoltan Trade hub event fixed - blue option will actually do something now
-Fixed: Quest beacon tooltips were sometimes innacurate
-More Typos/Grammar Fixes
Post edited January 22, 2013 by GregT_314
Yeah, I was wondering about the file version numbers. Thanks for this!
evanfolman: Yeah, I was wondering about the file version numbers. Thanks for this!
Everyone who is wondering about the confusing GOG numbering scheme should vote for this community wish:
Add version number to GOG releases, e.g. Earth 2140 (release 1.2)

Proposed scheme: <game-version-string>+gog<internal-version-number>

GOG, this would be highly appreciated & would reduce the amount of support tickets ! :)
Post edited February 09, 2013 by shaddim