Juzza, Thank you very much for the kind words!
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All right, I've done some revisions to the mod.
Enabled (i.e. commented out) units:
26 Light Cavalry
50 Slinger
39 Heavy Infantry
126 Woodsman
1118 Markata
Reason: Included in some national army lists, so that those lists do not get broken. Affected nations were the ape nations, nations with slingers (which can be useful, hence enabled again) and MA Man (has both slingers and light cav). The HI is enabled because it IS heavy infantry for EA and not utter crap. Woodsman was enabled because it gives some raiding potential for those who find them even if they lack national stealth units.
For people who are wondering why some indies are still enabled and some are not,
read the mod file. It has a fairly extensive commentary section in the beginning which contains the rationale for WHY things have been done the way they have and why for example indie Pale Ones are unmodded (they are amphibian, so they can allow expansion to water from land). I am a firm believer in the maxim that undocumented code is only half-finished at best, and that also means giving a brief explanation on design principles.
The goal of the mod was NOT to eliminate ALL independents completely, but to eliminate the useless crap and totally worthless hordes of chaff that the AI likes to build while preserving the better units and allowing some options. Militia number 31, which is available to MA Man will NOT be enabled. It stays at 9000 gold a pop because it can be found in no less than three poptypes and I refuse to mangle the purpose of the mod by allowing it. MA Man will just bloody well have to do without that unit. If you're playing MA Man and in such desperate straits that you need to recruit the militia instead of spearmen to serve as chaff and archer bait, there's no hope for you anyway and the mod stays truer to its purpose.
The mounted commanders were never affected by this mod because those poptypes are far less common than the infantry ones and the nations with crap leadership deserve SOME chance of finding good commanders. Militia #30, which can appear from "lucky" events (ok, sometimes it is lucky, but more often not) is unaltered so that it doesn't bankrupt anyone, but unfortunately it appears in three poptypes, so you WILL see some of it in the AI armies. But there will be less chaff than normal and none of the indie archer hordes unless the archers are national troops, longbows or woodsmen.
Note that the mod version and filename has not been changed, because I really can't be arsed to do that. Just replacing the mod file with the new version will overwrite things and change existing games on the fly. If you're using it in MP, make sure everyone changes it at the same time.
Hopefully this lengthy post answers most questions you may have.