Trick one: SVN and NTFSLink

Normally, thanks to HL2's inflexible directory structure limitation, you 
have to copy scene, sound, and material files in and out of your SVN tree 
when you update or change them. Well, no more! Go download NTFSLink 
( http://elsdoerfer.name/=ntfslink ).  This gives you a Windows equivalent 
of UNIX symbolic directory links, turning your directory structure from a 
rooted tree into a directed acyclic graph.  This means you can have 
folders inside your SNV tree operating as subfolders of your HL2 directory 
structure. Inside SVN, have separate directories for your sounds, scenes, 
materials, etc...

svn_root/
|- ourmaps/
|- oursounds/
|- ourscenes/
|- ourmaterials/

Under your hl2 directory, you'll need your usual subdirectories:
hl2/
|- maps/
|- sound/
|- scenes/
|- materials/

NTFSlink is a Windows Explorer shell extension.  Right-click and drag the 
svnroot/ourmaps/ directory into the hl2/maps/ directory, and select "Create 
junction here" (it has a green arrow icon).  Rename the resulting junction 
from "Link to ourmaps" to just "ourmaps".  Do the same for whatever other 
directories you need.  Now, the hl2 directory structure will think it looks 
like this:

hl2/
|- maps
|  |- ourmaps
|- sound
|  |- oursounds
|- scenes
|  |- ourscenes
|- materials
   |- ourmaterials

Congratulations! Now your HL2 subdirectories are directly under source 
control.


Trick two: getting your maya character into HL2

Ok, any students of good software engineering practices can leave the 
building now. It's all waterfall processes here: once you move on to a 
later step, you can't go back without invalidating all the work you've 
done.  Yeah, sucks to be you, but be very sure you like what you've got 
with one step before moving forward.

Step one: modeling.  The tools I was working with crashed on more than 
about ten thousand triangles ... boo. Even still, don't skimp around the 
eyes and mouth, and make sure you have internal mouth geometry. I had a 
25k-triangle model, and used Maya's simplify to cut it down. I ended up with 
three vertices on each eyelid, which was not nearly enough. I also had my 
teeth as separate shells, and that was also a mistake.

Step two: UVs. Make sure you like these before you commit - it's like a 
jigsaw puzzle. Dedicate a little more space, relatively, to the face than 
to anywhere else on the body.  Rumor has it that the actual Valve models 
have one texture just for the face, one for everything else. This may be a 
good idea. Resist the temptation to use the "unfold" button on the hands - 
it flattens it out nicely, but distorts it all to hell. Not worth it.

Step three: texturing. Make sure you have nice and distinct facial 
features, eyebrows, lips, and facial hair if applicable.  The more 
high-resolution photos you have to work from, the better.  Once you've got 
your textures, make sure they're saved as power-of-two-sized TGAs, inside 
your sourcesdk_content/.../materialsrc/ directory, and that Maya references 
those. Also, don't put any hyphens or underscores in the names. You also 
have to have at least one triangle with the Valve mouth texture, and one 
with their eye texture. (It's possible that you're actually supposed to 
create your own eye geometry and just put their eye texture on it, but I'm 
really not sure about this.)

Step four: Facial shapekeys.  VERY IMPORTANT: Resist the urge to do your 
skeleton rig before these!! I cannot stress this enough. This was the 
biggest mistake I made, and my character's face fell apart. Literally.  
Probably the easiest way to do these is to make a blendshape for each one, 
then key them all so the appropriate one is applied at the appropriate 
frame. Unfortunately, this makes your file *huge* and most graphics cards 
will start to choke. You have to grit your teeth and muscle through. It 
may well be just as possible to move the vertices around and key them 
individually, or even make some lattice deformers around the face and key 
them. If so, you're probably better off.

Step five: Rigging. Others have said much better things than I on this one. 
Be especially careful about getting the bones into the hand in the right 
place.

Step six: export from Maya. I used Prall's Tools with the .vta export 
patch and it seemed to work decently well.  They're not very good at 
ignoring things that aren't on the reference layer, though, so you may 
have to do some major trimming from the files you export. Fortunately, 
this step and step seven are intertwined enough that you can go back and 
forth until you get it right. In the VTA file you should have some header, 
then a ginormous list of vertices at each frame:

...
time 0
0 x y z nx ny nz
1 x y z nx ny nz
...
5786 x y z nx ny nz
time 1
0 x y z nx ny nz
1 x y z nx ny nz
...
time 35
0 x y z nx ny nz
...
5786 x y z nx ny nz
end

There should be one set of times for the skeleton, and one set of times for 
your vertices. If you have more than that, it grabbed your blendshapes and 
exported them too. Good times.

Step seven: import into HL2.  There are some pretty good tutorials on how 
to set up your .qc file and a .bat file to do the compile; QCEyes will give
you the extra parts to link in your .vta (though I never managed to get 
actual eyes). When you're deciding which character to replace, in 
single-player HL2 you actually have 21 males and 15 females to choose from. 
If you replace one in Group01, it'll be the "downtrodden" model; Group02 
is the "refugee" model, and Group03 is the "rebel" model.

Your character can do anything a citizen can do.  There are rumors that 
you can get animations from any character with the same rig by referencing 
a bunch of different files in your .qc, but I can't confirm this.