Here is a set of step-by-step instructions for reproducing the three basic mods (breast size, jiggle and headshot) that we can currently make work.
1) Download and unpack the updated Cryptic toolset I have posted. For purposes of this tutorial, I will assume you put it in the c:\Toolset folder.
2) If the toolset is for the current (or perhaps a recent) version of the game, you can skip this step and go to Step 3. But at some time in the future, you may need to rebuild the serialization library. To start, open an command window (Admin) in your c:\Toolset folder (or navigate there). All commands in this tutorial will be run inside a command window.
2a) Start the STO Launcher. Then run the command:
Gibbed.Cryptic.ExportSchemas
This should overwrite the files in c:\Toolset\schemas\Star Trek Online\Launcher\schemas with new versions.
2b) Start the STO Game Client (and close the launcher if it doesn't close). Run the command:
Gibbed.Cryptic.ExportSchemas
again. This should overwrite the files in c:\Toolset\schemas\Star Trek Online\Live\schemas with new versions. Close the Game Client.
2c) There is currently one schema file that creates problems. Go into your c:\Toolset\schemas\Star Trek Online\Live\schemas folder and delete the file "UIGenTestModelParse.schema.xml".
2d) Now (in the c:\Toolset folder) run the command:
Gibbed.Cryptic.GenerateSerializer --game=StarTrekOnline
This will generate a file Gibbed.StarTrekOnline.Serialization.dll in your c:\Toolset folder.
2e) Copy that file to the folder c:\Toolset\serializers\assemblies, and rename it "Newest.dll" (there is already a Newest.dll included with the toolset; if it works, you should have skipped steps 2a - 2e, so just delete or overwrite the existing "Newest.dll").
3) Make sure the Game Client is closed. Open a new command window (Admin) and navigate to the Star Trek Online\Live\piggs folder of your STO installation. If you have an "Unpack" folder here left-over from the last time you recompiled the mods, delete it completely now. Run the command
c:\Toolset\Gibbed.Cryptic.Unpack bins.hogg Unpack
In your command window, change directory into the piggs\Unpack\Bin folder you just created.
4) Now (in the piggs\Unpack\Bin directory) extract the .xml files to be modified by running the following four commands:
4a) c:\Toolset\Gibbed.Cryptic.ConvertResource -x headshotinfos.bin
4b) c:\Toolset\Gibbed.Cryptic.ConvertResource -x scaleinfos.bin
4c) c:\Toolset\Gibbed.Cryptic.ConvertResource -x skelinfos.bin
4d) c:\Toolset\Gibbed.Cryptic.ConvertResource -x dynbouncer.bin
The first is for the headshot mod. The second is for the breast size mod. The last two are for jiggle. If you don't want all three mods, you can skip the ones you don't need.
5) There are exactly four xml files that are modded to produce the three basic mods. Generally they will not change between updates, so I just keep my versions - with my preferred breast size and jiggle settings - in a sub folder of Star Trek Online\Live\piggs so I don't have to re-extract them or edit them every time. Password42 included instructions for customizing the jiggle and breast size mods in his last official release, and he provided "presets" you can simply use without modification.
6) For the headshot mod, take the working version of headshotinfos.bin that I posted (or the one from Password's last release), put it in a throwaway folder somewhere, and (in a command prompt (Admin) window in that folder) run the command:
c:\Toolset\Gibbed.Cryptic.ConvertResource -x headshotinfos.bin
Then navigate down to the Headshotinfos\Defs\Skel_Infos subfolder you just created with that command and grab the file "Startrekmaleheadshot.xml" (only). Save that file somewhere that you can use the next time you regenerate the mod, and also copy it to your piggs\Unpack\Bin\Headshotinfos\Defs\Skel_Infos folder (overwrite the version that's there). Finally (in your piggs\Unpack\Bin folder) run the command:
c:\Toolset\Gibbed.Cryptic.ConvertResource -b Headshotinfos
Copy the new Headshotinfos.bin file you just created from that folder to Live\localdata\bin to install it for use. Note that the addition of new NPC conversations in new content "breaks" the headshot info mod, in that the new conversations won't work properly if you have an old modded version in you localdata\bin folder.
7) For the breast-size mod, the one file which is modified is Unpack\Bin\scaleinfos\Startrekfemalescalegroups.xml. Password's last release explained the which parameters in this file he changed, and he also provided presets, so I won't duplicate the instructions. As before, I keep a saved copy of this file so I can easily retrieve it when I need to recompile everything. Copy your modified version of Startrekfemalescalegroups.xml to the Live\piggs\Unpack\Bin\scaleinfos\ folder, then (in your piggs\Unpack\Bin folder) run the command:
c:\Toolset\Gibbed.Cryptic.ConvertResource -b Scaleinfos
Copy the new Scaleinfos.bin file you just created from that folder to Live\localdata\bin to install it for use.
8) For the jiggle mod, there are two files modified, although one of them never changes and is independent of settings. The file piggs\Unpack\Bin\skelinfos\Startrekfemale.xml has a trivial modification: change the line containing "<BouncerInfo>" so it reads like this:
<BouncerInfo>test</BouncerInfo>
Don't change anything else in the file. This points the jiggle physics to a *second* file, which actually contains the jiggle settings. This second file, test.xml, was also provided by Password42 in the last release, and he provided instructions for how to modify it to customize jiggle that I won't repeat here. Copy the version of test.xml with your preferred jiggle settings to the folder piggs\Unpack\Bin\dynbouncer\. Then (in your piggs\Unpack\Bin folder) run the following two commands:
c:\Toolset\Gibbed.Cryptic.ConvertResource -b Skelinfos
c:\Toolset\Gibbed.Cryptic.ConvertResource -b Dynbouncer
Copy the modified versions of Skelinfos.bin and Dynbouncer.bin to your Live\localdata\bin folder to install them for use.
9) That's it! As I mentioned, it is convenient to save copies of the four xml files that are actually modified, so you can easily re-use them. You can delete the piggs\Unpack folder created in Step 3 (and everything in it) if you want to save disk space. You can't re-use it with future versions of the client, so there is no real advantage to keeping it.