The vanilla source code (version 1.06) can be found at least here:

http://icculus.org/twilight/darkplaces/files/id1qc.zip

C0burn had also linked Ultimate Regular Quake Patch's source code to me. It has a lot of fixes/workarounds for problems that may arise with the vanilla code. I borrowed some code from it for one of my maps.

http://www.quaketastic.com/files/misc/urqp106a.zip

Good luck to your plunge! :) 

Looks like a lot of MP focus in that second link. Thank you! 

For my own purposes I put some QuakeC onto github a while back. There's various places to get these same things, but:

For the original 1.06 QuakeC you can browse it here: https://github.com/neogeographica/quakec/tree/1.06

or download a zip of it from here: https://github.com/neogeographica/quakec/archive/1.06.zip

For Preach's cleaned-up 1.06 you can browse here: https://github.com/neogeographica/quakec/tree/1.06_Preach

or download here: https://github.com/neogeographica/quakec/archive/1.06_Preach.zip

And you can see the differences between them here: https://github.com/neogeographica/quakec/compare/1.06...1.06_Preach 

Eh, one caveat that just occurred to me about those zipfile downloads. If you get the code that way then all the files will use Unix-style line endings. Might cause you issues depending on what text editor you're using. 

The URQP package is neat. I didn't know that that was where the Quake Info Pool fixes ended up. 

I've updated the QuakeWiki with a list of bugs I know about in the 1.06 code.

https://quakewiki.org/wiki/Quake_bugs

It's most of the URQP stuff, plus other bits and bobs.

Please amend or ask me to amend if anything is missing! 

Quote from your list:

Rotfish does not become non-solid until the final frame of it's death animation * this is not in line with other monsters, so it is considered a bug

Correct me if I'm wrong, but don't fiends exhibit similar behaviour, too? 

They become non-solid on frame 6/9!

Glancing at some others quickly, hellknight is frame 3, as is the grunt.

I think it should be harmonised. 

Should we class unused content, such as the death knight grunt sound and unused animations and unused shub sounds, as a "bug"? There's other bits and pieces as well, including unused animations in the knight, soldier and ogre. Can we introduce these in a non gameplay changing manner? Should they be an optional spawnflag/worldspawn flag? 

In the ai.qc i took the ai_run part.

===
void(float dist) ai_run =
{
local vector delta;
local float axis;
local float direct, ang_rint, ang_floor, ang_ceil;
local entity spot; //xogre_leak code
movedist = dist;
// see if the enemy is dead
if (self.enemy.health <= 0)
{
self.enemy = world;
spot = find (world,classname,"monster_xogre");

if ( spot ) {find (world,classname,"monster_xogre");
{
spot.think = xogre_leak1;
spot.leakentity = self;
}
}


and the bastard lays it's blame on me!

Thanks Spike, that was right on target!
Now see if I can switch leak with laughing. 

Thunderbolt bugs relating to the "three beams"

I assume this bug isn't related to lightning attacks (both thunderbolt and shambler) being able to damage entities through walls? Also, hitchecks with the thunderbolt are kinda weird. (You probably know what I mean with that, but if you don't, just tell me, and I can explain in a reply.)

multiple megahealth rots down too quickly (double rot)

I had learned about this actually, when I tried to make a custom Doom-like health bonus item. My health would rot down super fast after having picked up like ten of those items! @~@ I actually thought that it was a feature, to make supercharged players less OP, or something. :D

targets not fired if the player doesn't take the item (e.g. already has max armour, touching armour should trigger a monster/something, but doesn't)

This is even more so arguable, whether it's a bug or not. I actually prefer it the current way. If I wanted to make 100 % sure about the targets being triggered when touching the item, I'd add a trigger_once brush or something.

(Also there are minor typos here and there in the list.) 

Thanks. I wasn;t aware Preach had a version of his own. I'll most likely use Preach's 106 code when I dive back in. I am using FTEQCCGUI and Notepad++ 

@dumptruck
Last year muk0r put together a "clean QC source"... but the readme doesn't say if there is any bugfixes :(
http://www.quaketastic.com/files/Clean_QuakeC_Source.zip

but maybe (i said maybe because i don't know if you want these features) you should start with custents?
http://www.quaketastic.com/files/tools/windows/quakec/custents.zip
It seems to be a mix of all the cool features of the two official mission-packs, like: rotating brushes, earthquakes, particle fields, breakable walls, etc 

Thanks for these links. I am looking at adding some of the custents features for sure. 

I think the "same name texture" crash mentioned on that page is only in GLQuake and derived engines. 

I agree about the item not triggering it's targets if it hasn't been picked up, that is definitely not a bug, it makes total sense for an item to not do anything if the player touches it but can't interact with it for whatever reason, like if their ammo is full or they have full armor or they already have that type of key in their inventory. Not to mention that a vast majority of maps are designed around this mechanic one way or another, like key traps triggering when the player, you know, picks up the key or encounters that get triggered when you pick up a particular weapon or powerup like quad damage

Now if we're talking about keeping the player from picking something up if they already have enough of it that's another story, it would definitely be nice sometimes if some things like ammo or health only gave themselves to you if you actually needed that much, it would definitely help prevent wastefulness by picking them up on accident when you don't really need that much yet 

I agree about the item not triggering it's targets if it hasn't been picked up, that is definitely not a bug, it makes total sense for an item to not do anything if the player touches it but can't interact with it for whatever reason, like if their ammo is full or they have full armor or they already have that type of key in their inventory. Not to mention that a vast majority of maps are designed around this mechanic one way or another, like key traps triggering when the player, you know, picks up the key or encounters that get triggered when you pick up a particular weapon or powerup like quad damage

Now if we're talking about keeping the player from picking something up if they already have enough of it that's another story, it would definitely be nice sometimes if some things like ammo or health only gave themselves to you if you actually needed that much, it would definitely help prevent wastefulness by picking them up on accident when you don't really need that much yet 

I should mention that the changes in the cleaned up code are only to eliminate compiler warnings, there aren't any bug fixes or behaviour changes. Just wanted to set the right expectations for it. 

Thanks for the clarification. I am still very much in the copy and paste fingers crossed stage of qc. I believe c0burn wants to release a bug smashed version of the code eventually. That's a great project IMO. 

Result is that a player in fight with an Axe_ogre will get pissed. If player is shot from distance, the ogre won't walk to the player's body. 

the point of doing it in ai_run is that:
a) self is the ogre that should do the widdle. there is absolutely no need to call find (because you can just use self). there is no need to loop etc (each monster will call the function at some point anyway).
however, you really ought to only do that logic if self.classname is actually what you expect. you don't really want scrags trying to widdle.
b) the player that its trying to urinate on is already stored inside self.enemy. This means that you don't need a seperate leakentity field - just use self.enemy! (do note that you'll want to avoid the self.enemy=world line if the ogre is meant to start widdling.) 

Thanks for your answer. Sorry I'm such a noob at coding.
If I use the self argument, how do I make it fit in?

As it is an experimental src, so maybe it is better to show an example
of what I am trying to do.
MF_Qtest00 

here's a demo of Qtest

the main problem, the "new" monsters seem too much overpowered (especially vomitus)

noticed a couple of issues, check the demo

http://quaketastic.com/files/demos/spy_MadfoxQtest_demo.rar 

Just finished a nice trick to change the serpent into a quaddam.
But don't touch it, cause it lives.., a bit husling with the skin file.

Yes, the src has a MISSILE weaponcode for each monster,
wizard is also much too strong. Number code for weapons won't work. Still beta.

Thanks for the demo, I'll look at it! 

You made your way quiet advanced on hard skill. Spy.
The missing sounds are qc depended.
I turned a bit strayed with the qtest.qc. adding the monsters,
especially the dragons, caused a lot of changes.

I assume the forced demo end had something to do with crashing,
it is still beta version, already glad it runs.

Thanks for taking your time.