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The "ReadMe" file makes mention of some changes to generals' and legendary units' ratings, special abilities, etc. Among these was giving the ten new special abilities to a number of them, sometimes replacing a pre-existing ability. This was too much detail to include in the patch documentation, but for those who are interested here is a precise breakdown of who got what.

First, as listed in the documentation, these are the new bios (which always provide information that enables us to assign more accurate ratings and teachable abilities):

USA:
Ambrose E. Burnside, Philip St. George Cooke, Thomas L. Crittenden, Jefferson C. Davis, Alfred Duffié, George W. Getty, John Gibbon, Gordon Granger, Alexander Hays, Philip Kearny, Rufus King, John A. McClernand, Irwin McDowell, Wesley Merritt, James Nagle, Richard J. Oglesby, Peter J. Osterhaus, John A. Rawlins, Phil Sheridan, Charles F. Smith, William F. Smith, George D. Wagner, Lew Wallace, William H.L. Wallace
CSA:
George T. Anderson, Robert Houston Anderson, John C. Carter, Philip St. George Cocke (revised bio), Philip Cook, Montgomery D. Corse, Arnold Elzey, Robert S. Garnett, States Rights Gist, Elkanah B. Greer, John B. Grayson, William P. Hardeman, John B. Hood, William Y.C. Humes, Benjamin G. Humphreys, John D. Imboden, Evander M. Law, Lunsford L. Lomax, Armistead L. Long, Dandridge McRae, William McRae, Albert Pike, Gideon J. Pillow, Gabriel J. Rains, Albert Rust, Stand Watie

Here is a list of all the generals who received new or different special abilities (not all of which are one of the new ones). A number indicates that one was replaced, while a + indicates an ability was added: so, for example, E.P. Alexander had one original ability replaced and two others added. Below I indicate which of the ten new abilities they got.
Edward P. Alexander (1, +2), John M. Brannan (+1), Ambrose Burnside (2), Joshua Chamberlain (1), Patrick Cleburne (1), Philip St. George Cocke (+1), Douglas H. Cooper (1), Abner Doubleday (1), Jubal Early (1), John B. Gordon (+4), Ulysses S. Grant, Winfield S. Hancock (1), A.P. Hill (1), D.H. Hill (1), John B. Hood (2), Henry J. Hunt (2, +1), Stonewall Jackson (1), Joseph Johnston (1), Robert E. Lee (1), Nathaniel Lyon (+1), John Magruder (1), George McClellan (1), Irwin McDowell (1), Benjamin McCulloch (+1), William N. Pendleton (1), John Pope (+1), Sterling Price (1), Robert E. Rodes (+1), William T. Sherman (1), Edmund K. Smith (1), George Thomas (1), August von Willich (1), Stand Watie (2, +1)

To see which generals and LU's got the new special abilities, it's necessary to know the number assigned each ability:
26 Thrifty (Attacks use only 1 point of supply, infantry and artillery only)
27 Stalwart (While unit is Fresh it takes only 1/10th normal morale loss from fire attacks, infantry and cavalry only)
28 Rangers (Reduces cost to enter a hex by 1 if the terrain cost is 3 or more, infantry only)
29 Cautious (Reduces damage this unit takes and causes in fire combat by 25%, infantry and artillery only)
30 Aggressive (Increases damage this unit takes and causes in fire combat by 25%, infantry and artillery only)
31 Tenacious (When in a pin-position with another unit, both units are automatically pinned, infantry only)
32 Hill Defenders (retains good morale defending a hill, infantry only)
33 Uphill Charger (what it sounds like, infantry only)
34 Efficient Fire (artillery can take an extra shot, like dragoon tactics)
35 Anti-Battery (artillery harms other artillery)

New special abilities used for generals with historically-based ratings/abilities (“new bio” indicates a general who previously did not have historically-based ratings):
26 Alexander, Elzey (new bio), Long (new bio), Magruder, E.K. Smith
27 Jackson, Kearny (new bio; made 25-percenter and given historical ratings/abilities), Osterhaus (new bio), C.F. Smith (new bio), Imboden (new bio)
28 Cooper, McCulloch, Watie (new bio; made 25-percenter and given historical ratings/abilities)
29 Cooke (new bio; made 25-percenter and given historical ratings/abilities), J. Johnston, McClellan, McDowell, L. Wallace (new bio)
30 Anderson (new bio), Early, Gordon (new bio; made 25-percenter and given historical ratings/abilities), Grant, A.P. Hill, Lee, Pope, Sherman, W.H.L. Wallace (new bio)
31 Doubleday, Gibbon (new bio), Oglesby (new bio), Rodes
32 Chamberlain, Cleburne, Hancock, D.H. Hill, Hunt, Lyon, Thomas
33 Price, Willich
34 Alexander, Brannan, Getty (new bio), Hunt, Pendleton
35 Alexander, Hunt

These Legendary Units got one of the new special abilities:
26 Jackass Regiment, Rockbridge Artillery, Extra Billy Smith’s Boys
27 Cameron’s Dragoons, Leadmine Regiment, Bethel Regiment, Lee’s Foreign Legion
28 Sykes’ Regulars, Invincible Guards
29 Wallace’s Zouaves, Pelican Rifles
30 Harvard Regiment, Old Vermont Brigade, Cox’s Wildcats, Ragged Old First
31 2nd Texas Sharpshooters, Chicago Irish Brigade
32
33
34 Chicago Mercantile Battery, Washington Artillery
35 Jeff Davis Battery, Richmond Howitzers, Jackass Regiment

This was all just a start, since we wanted to get the ten new special abilities into the game. If I missed any generals or LU's who deserve one or more of these new abilities please make a suggestion here.

I am happy to see FOF continue to improve.  My congradualtions. 
 
Everyone has their favorite commander and can edit the abilities.  My interest is in George Thomas, USA.  Civil War Generalship, William J. Wood, makes an excellent arguement that he was of the caliber of Lee, Grant and Sherman.  Indeed, Mr. Wood suggests that Gen. Thomas was superior as a field commander. I do not mention Wood's work to dispute your rankings, I have done my personal edits.  I merely wanted to "extend the debate."  Thank you.

cerosenberg,
It's good to see you back in these parts. I hear you on Thomas. We still need to have a bio for him done, and at that time I'd be revisiting his ratings and abilities. (Also, I'll soon be reading the definitive book on Mill Springs, and expect to learn about his earlier role in the war.)