Here's a list of files which have been changed from stock - note that additional files I've added might also cause compatibility issues, but the chances are much less likely.

This list is current as of 1.0.11

nrm2\common
nrm2\common\ai_equipment
nrm2\common\ai_equipment\ENG_naval.txt
nrm2\common\ai_equipment\FRA_naval.txt
nrm2\common\ai_equipment\generic_naval.txt
nrm2\common\ai_equipment\GER_naval.txt
nrm2\common\ai_equipment\ITA_naval.txt
nrm2\common\ai_equipment\JAP_naval.txt
nrm2\common\ai_equipment\USA_naval.txt
nrm2\common\ai_strategy
nrm2\common\ai_strategy\♥♥♥.txt
nrm2\common\bookmarks
nrm2\common\bookmarks\blitzkrieg.txt
nrm2\common\country_leader
nrm2\common\country_leader\00_traits.txt
nrm2\common\decisions
nrm2\common\decisions\ENG.txt
nrm2\common\ideas
nrm2\common\ideas\britain.txt
nrm2\common\ideas\canada.txt
nrm2\common\ideas\czechoslovakia.txt
nrm2\common\ideas\germany.txt
nrm2\common\ideas\netherlands.txt
nrm2\common\ideas\romania.txt
nrm2\common\ideas\usa.txt
nrm2\common\ideas\zzz_generic.txt
nrm2\common\modifiers
nrm2\common\modifiers\00_static_modifiers.txt
nrm2\common\national_focus
nrm2\common\national_focus\germany.txt
nrm2\common\national_focus\india.txt
nrm2\common\national_focus\japan.txt
nrm2\common\national_focus\netherlands.txt
nrm2\common\national_focus\uk.txt
nrm2\common\national_focus\usa.txt
nrm2\common\scripted_effects
nrm2\common\scripted_effects\USA_scripted_effects.txt
nrm2\common\technologies
nrm2\common\technologies\artillery.txt
nrm2\common\technologies\electronic_mechanical_engineering.txt
nrm2\common\technologies\MTG_naval.txt
nrm2\common\technologies\naval.txt
nrm2\common\terrain
nrm2\common\terrain\00_terrain.txt
nrm2\common\unit_leader
nrm2\common\unit_leader\00_traits.txt
nrm2\common\units
nrm2\common\units\equipment
nrm2\common\units\equipment\convoys.txt
nrm2\common\units\equipment\ship_hull_carrier.txt
nrm2\common\units\equipment\ship_hull_cruiser.txt
nrm2\common\units\equipment\ship_hull_heavy.txt
nrm2\common\units\equipment\ship_hull_light.txt
nrm2\common\units\equipment\ship_hull_submarine.txt
nrm2\common\units\names_ships
nrm2\common\units\names_ships\JAP_ship_names.txt
nrm2\common\units\names_ships\SOV_ship_names.txt
nrm2\common\units\battlecruiser.txt
nrm2\common\units\battleship.txt
nrm2\common\units\carrier.txt
nrm2\common\units\destroyer.txt
nrm2\common\units\heavy_cruiser.txt
nrm2\common\units\light_cruiser.txt
nrm2\common\units\submarine.txt
nrm2\events
nrm2\events\MTG_Netherlands.txt
nrm2\gfx
nrm2\gfx\interface
nrm2\gfx\interface\equipmentdesigner
nrm2\gfx\interface\equipmentdesigner\ship_designer_popup_bg.dds
nrm2\gfx\interface\navalcombat
nrm2\gfx\interface\navalcombat\ships
nrm2\gfx\interface\navalcombat\ships\battlecruiser_I.dds
nrm2\gfx\interface\navalcombat\ships\battlecruiser_II.dds
nrm2\gfx\interface\navalcombat\ships\battlecruiser_III.dds
nrm2\gfx\interface\navalcombat\ships\battlecruiser_IV.dds
nrm2\gfx\interface\navalcombat\ships\battleship_I.dds
nrm2\gfx\interface\navalcombat\ships\battleship_II.dds
nrm2\gfx\interface\navalcombat\ships\battleship_III.dds
nrm2\gfx\interface\navalcombat\ships\battleship_IV.dds
nrm2\gfx\interface\navalcombat\ships\carrier_I.dds
nrm2\gfx\interface\navalcombat\ships\carrier_II.dds
nrm2\gfx\interface\navalcombat\ships\carrier_III.dds
nrm2\gfx\interface\navalcombat\ships\carrier_IV.dds
nrm2\gfx\interface\navalcombat\ships\destroyer_I.dds
nrm2\gfx\interface\navalcombat\ships\destroyer_II.dds
nrm2\gfx\interface\navalcombat\ships\destroyer_III.dds
nrm2\gfx\interface\navalcombat\ships\destroyer_IV.dds
nrm2\gfx\interface\navalcombat\ships\heavy_cruiser_I.dds
nrm2\gfx\interface\navalcombat\ships\heavy_cruiser_II.dds
nrm2\gfx\interface\navalcombat\ships\heavy_cruiser_III.dds
nrm2\gfx\interface\navalcombat\ships\heavy_cruiser_IV.dds
nrm2\gfx\interface\navalcombat\ships\light_cruiser_I.dds
nrm2\gfx\interface\navalcombat\ships\light_cruiser_II.dds
nrm2\gfx\interface\navalcombat\ships\light_cruiser_III.dds
nrm2\gfx\interface\navalcombat\ships\light_cruiser_IV.dds
nrm2\gfx\interface\navalcombat\ships\sh_battleship_I.dds
nrm2\gfx\interface\navalcombat\ships\sh_battleship_II.dds
nrm2\gfx\interface\navalcombat\ships\sh_battleship_III.dds
nrm2\gfx\interface\navalcombat\ships\sh_battleship_IV.dds
nrm2\gfx\interface\navalcombat\ships\submarine_I.dds
nrm2\gfx\interface\navalcombat\ships\submarine_II.dds
nrm2\gfx\interface\navalcombat\ships\submarine_III.dds
nrm2\gfx\interface\navalcombat\ships\submarine_IV.dds
nrm2\gfx\interface\technologies
nrm2\gfx\interface\technologies\advanced_submarine.dds
nrm2\gfx\interface\technologies\basic_carrier.dds
nrm2\gfx\interface\technologies\early_carrier.dds
nrm2\gfx\interface\technologies\semi_modern_submarine.dds
nrm2\gfx\interface\technologies\sonar.dds
nrm2\history
nrm2\history\countries
nrm2\history\countries\ARG - Argentina.txt
nrm2\history\countries\AST - Australia.txt
nrm2\history\countries\BRA - Brazil.txt
nrm2\history\countries\CAN - Canada.txt
nrm2\history\countries\CHI - China.txt
nrm2\history\countries\CHL - Chile.txt
nrm2\history\countries\COL - Colombia.txt
nrm2\history\countries\CSA - CSA.txt
nrm2\history\countries\DDR - East Germany.txt
nrm2\history\countries\DEN - Denmark.txt
nrm2\history\countries\ENG - Britain.txt
nrm2\history\countries\EST - Estonia.txt
nrm2\history\countries\FIN - Finland.txt
nrm2\history\countries\FRA - France.txt
nrm2\history\countries\GER - Germany.txt
nrm2\history\countries\GRE - Greece.txt
nrm2\history\countries\HOL - Holland.txt
nrm2\history\countries\ITA - Italy.txt
nrm2\history\countries\♥♥♥ - Japan.txt
nrm2\history\countries\LAT - Latvia.txt
nrm2\history\countries\MEX - Mexico.txt
nrm2\history\countries\NOR - Norway.txt
nrm2\history\countries\NZL - New Zealand.txt
nrm2\history\countries\POL - Poland.txt
nrm2\history\countries\POR - Portugal.txt
nrm2\history\countries\PRU - Peru.txt
nrm2\history\countries\ROM - Romania.txt
nrm2\history\countries\SAF - South Africa.txt
nrm2\history\countries\SIA - Siam.txt
nrm2\history\countries\SOV - Soviet union.txt
nrm2\history\countries\SPR - Spain.txt
nrm2\history\countries\SWE - Sweden.txt
nrm2\history\countries\TUR - Turkey.txt
nrm2\history\countries\URG - Uruguay.txt
nrm2\history\countries\USA - USA.txt
nrm2\history\countries\USB - USB.txt
nrm2\history\countries\WGR - West Germany.txt
nrm2\history\countries\YUG - Yugoslavia.txt
nrm2\history\units
nrm2\history\units\ARG_1936_naval_mtg.txt
nrm2\history\units\AST_1936_naval.txt
nrm2\history\units\BRA_1936_naval.txt
nrm2\history\units\CAN_1936_naval_mtg.txt
nrm2\history\units\CAN_destroyers_for_bases_mtg.txt
nrm2\history\units\CHI_1936_naval_mtg.txt
nrm2\history\units\CHL_1936_naval_mtg.txt
nrm2\history\units\COL_1936_naval_mtg.txt
nrm2\history\units\DEN_1936_naval_mtg.txt
nrm2\history\units\ENG_1936_Naval.txt
nrm2\history\units\ENG_destroyers_for_bases_mtg.txt
nrm2\history\units\FIN_1936_naval_mtg.txt
nrm2\history\units\FRA_1936_naval_mtg.txt
nrm2\history\units\GER_1936_naval_mtg.txt
nrm2\history\units\GRE_1936_naval_mtg.txt
nrm2\history\units\HOL_1936_naval_mtg.txt
nrm2\history\units\ITA_1936_naval_mtg.txt
nrm2\history\units\JAP_1936_naval.txt
nrm2\history\units\LAT_1936_naval_mtg.txt
nrm2\history\units\MEX_1936_naval_mtg.txt
nrm2\history\units\NOR_1936_naval_mtg.txt
nrm2\history\units\POL_1936_naval_mtg.txt
nrm2\history\units\POR_1936_naval_mtg.txt
nrm2\history\units\PRU_1936_naval_mtg.txt
nrm2\history\units\ROM_1936_naval_mtg.txt
nrm2\history\units\SIA_1936_naval_mtg.txt
nrm2\history\units\SOV_1936_naval_mtg.txt
nrm2\history\units\SPR_1936_naval_mtg.txt
nrm2\history\units\SWE_1936_naval_mtg.txt
nrm2\history\units\TUR_1936_naval_mtg.txt
nrm2\history\units\URG_1936_naval_mtg.txt
nrm2\history\units\USA_1936_naval_mtg.txt
nrm2\history\units\YUG_1936_naval_mtg.txt
nrm2\interface
nrm2\interface\countryproductionlineview.gui
nrm2\interface\countrytechtreeview.gui
nrm2\interface\equipmentdesignerview.gui
nrm2\interface\frontendgamesetupview.gui
nrm2\interface\frontendmainview.gui
nrm2\interface\frontendmainviewbg.gfx
nrm2\interface\load_screen.gfx
nrm2\interface\load_screen.gui
nrm2\interface\naviesview.gui