I understand your confusion.
As I understand it, the timeline of the various versions looks like this:
*
Privateer Remake (PR) -- newest release is v1.2, which is from 2005.
*
Wing Commander Universe (WCU) -- newest release is v0.2a, which is from 2005. WCU re-uses and expands on Privateer Remake and makes the wider Wing Commander Universe star systems and ships available.
WCU is described as being "A Privateer style game with Wing Commander ships, set in the Wing Commander Universe. The year is 2669, you have complete freedom to do what YOU want. choose your own destiny as either a male/female human, Kilrathi or firekkan as you travel the universe."
A slightly different take on the goals and features of WCU is available on the dedicated
WCU site.
Privateer Remake suffered a reportedly acrimonious split into two forks:
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Privateer Gemini Gold (GG) -- newest release is v1.03, which is from December 2009 (various patches are floating around). Attempts to be a faithful recreation of the original Privateer. The
Privateer Remake purist's choice if you will.
*
Privateer: Parallel Universe (PPU) -- chuck_starchaser's spiritual successor to PR, which adds more ships from WCU while adding features that are not found in GG (turret AI, new quests, flyable draymans/confederate fighters/stillettos, updated ship variants, among others). Does not include the expanded WCU star systems.
PPU was hosted on a forum with an associated version control repository hosting both the source code and the playable binaries which is unfortunately no longer available. As such, the last available copy of PPU is the one hosted on the download sites you mention. These copies run on Windows. These copies also unfortunately use an outdated version of the
VegaStrike Windows binaries.
In the
Frankenstein's Monster is Alive! thread, travists attempted to create an updated hybrid of PPU and WCU. I believe he originally attempted to make (parts of) WCU run on GG as well.
With inspiration from travists' work, I took the latest version of PPU, ripped out the outdated Windows stuff and (among other things) updated it to run with the newest (Linux) version of the
VegaStrike engine. Since travist's intention was to revive
Wing Commander Universe, I named my PPU rework
Privateer: Wing Commander Universe (PWCU). The goal was to eventually re-use as much of the WCU content as would make sense, as it would be a shame to see it just sit and suffer from bit rot.
At present, I have not integrated the wider WCU content in my PWCU project. Therefore PWCU is currently roughly equivalent to the old PPU and possibly slightly more playable -- at least it was when last I played it. IIRC I was doing the Black Rhombus mission in the Oxford system and was having my ass handed to me by a very well armored Galaxy. One of the things I put particular emphasis on reworking was the IMHO broken automatic ship upgrade system, which now no longer makes opponent ships use completely improbable upgrades. We're talking a level_5 reactor + level_5 shield generator + 3 heavy guns on a light ship which should
at most support a level_1 reactor + shield generator + light gun upgrades. Prior to this rework, the upgrade system was in my experience thus making opponent ships effectively impossible to kill unless one used the dev ship.
Currently, PWCU does not run on Windows. I have so far failed to successfully build the requisite
VegaStrike and
Python binaries and the binaries supplied by the
VegaStrike project do not run my PWCU code. I sort of ran out of motivation to investigate this any further, as I could play just fine on Linux.
I hope that at least clears things up a little?