I don't really have a document per-se, but more like just a collection of verbally communicated rules that we all just keep track of mentally.

For feats, i remove 90% of the "expected" feats and just make them standard options. Things like power attack, combat expertise, two weapon fighting, are all unlocked for free as long as you meet the prerequisites. So anyone with 13 strength can power attack, anyone with 15 dex has reduced twf penalties, anyone with 6 bab and 17 dex gets a second offhand attack, anyone with 13 int can get 1:1 AC to attack penalty up to their bab or 5.

Things like improved sunder/trip etc are still feats, as they improve the thing you can already do.

Prerequisites for prestige classes are largely removed, but instead are entered into entirely by RP and in character decision making. The more you work with the DM on this, the better it will work out. I have and will design entire prestige classes for a campaign, just for one player, that may never see use again, but is tailored directly to your character's story. I'm usually quite generous on this front too, so you can probably expect said prestige class to be stronger than most others, but I need you to work with me narratively for this to succeed.

Players can still take prestige classes normally if they wish, unless it's inappropriate for the campaign in question. You probably won't be going incanter if the campaign is set in the dark ages, where magic is a crime punishable by death, and mages rarely ever get past level 3 for example.

I use an optiona gestalt system that players can engage in. For e6 it allows players to begin gestalting at 6 instead of taking feats, but once they begin gestalting they must continue to gestalt until 6//6, and once they reach 6//6 they become permanently considered ECL7, meaning they will forevermore gain less xp than their level 6 counterparts.

Generally speaking, I will allow users to use either the pathfinder or the 3.5 version of something, but they cannot mix and match. For example, you cannot use the pathfinder unchained rogue in combination with a 3.5 ACF, nor can you use a pathfinder archetype with a 3.5 base class, even if the class has all the class features replaced by said ACF/archetype.

Campaigns may have limitations or subsystems included or enforced on a per campaign basis, I may for example, do a words of power campaign, or a spheres of power campaign, where all casters, player or npc, must utilize that system, but outside of those circumstances, generally speaking anything goes.

Druids are almost universally not an acceptable choice as a player class, as they are bound by duty to protect their territory in my setting. They only really work if a campaign is largely stationary. Deal with it.

There's probably a tonne more, I didn't bother with the specifics of character creation, as that's not really house rules, just cherry picked optional rules usually.