Current PCGen implementation is an evolving use on Archetype Category exclusion based upon a "TYPE". However, the earlier design was based on global class features, but failed to capture the local class features which cause overlap issues.
Class Feature - Fighter Bonus Feats
Global is "Bonus Feats", Local was "Fighter Bonus Feat 2" removes the Level 2.
The FACT system clearly distinguishes these two classifications:
Fighter_Archetype_BonusFeats - Global Class Feature identification
Fighter_CF_BonusFeat2 - What Global or Local Portion to swap out.
Core Rulebook - has the base classes
Advanced Player's Guide
Advanced Class Guide
Advanced Race Guide
All base classes in the core and the core supplements.
Some strangling systems will be found and tackled later.