UPD:
http://www.gog.com/forum/disciples_series/fresh_start Backup 3 exe files for RotE. Install RotE Gold upgrade and then RotE 3.01 patch. Restore 3 exe files for RotE. I post somewhere link to mine exports fodlers with combined compatible maps. You need Impire.sg file that the only one keep missed after you update RotE GOG version.
Use offline builds. Even for GOG Galaxy you can install offline and Galaxy find them. Offline version have more content than Galaxy build.
To install old retail offline patches i mention here - check my link above and find REGEDIT entry that patches look for.
THAT should be enough for fresh start with GOG versions.
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DisciplesGL is a mod. And it change too much. For first experience i recommend Steam version + GCFScape tool to extract game from Steam Valve VPK archives to get proper client, copy GOG 6 exe files +1 manual to Steam version.
Copy 16 maps from GR to RotE and 19 maps from RotE to GR (maps stored in Export folders where also heroes). Copy 12 leaders from GR to RotE and probably one hero from RotE to GR (archangel, any others heroes not compatible from RotE to GR).
Heroes from RotE NOT COMPATIBLE with GR. And for you own heroes even GR hero not be compatible with RotE. be careful with that, you cant start some scenraios\campaign in one version and continue in another.
Or if you still want GOG version (Steam require some tweaking to make game DRM-free) - download and install RotE Gold Upgrade from topic i linked above /does_the_gog_version_of_disciples_2_contain_rise_of_the_elves_gold
That one should be fine to make GOG almost proper build (still be missed Impire singleplayer map for Empire faction that should be included in any Gold editions because it be part of GR from 2003).
GOG version "as is" same as Steam is 3.00 and not 3.01 (steam also 2.00 instead of 2.02, but GOG already 2.02 here). That installer reported as fix that and also update the game (because GOG partially patched already, for else versions that Gold Upgrade is not 3.01 patch)
GOG Galaxy current build still MISS 12 blank heroes in GR for english version. Offline installer (did you know where to get them?) current build have them, but no Galaxy. Should be 12 .ldr files in Export folder for GR game.
here the link to unofficial GOGdb site where you can see that 12 .ldr is missing from online builds:
http://www.gogdb.org/product/1207663703#builds http://www.gogdb.org/manifest/73489d9306839a9290c4a6b9cfe3fa63 here the POL version of GOG Galaxy online build - and there is more files under Export folder
http://www.gogdb.org/manifest/d0489b0a412e4ec51d8a4d91fe658e60 (still any GOG miss some files). Additional technical info about GOG releases:
http://www.gogdb.org/products?search=disciples Here the (almost accurate, should be more Tutorials and one map with minor misprint name) list of maps from each editions:
http://nevendaar.com/index/0-43 (sorry, russian discs boxart, there is list on english site, but only list without any formating and any boxarts at all, list is based on origianl English version anyway - i double checked it compared to CDs)
RotE support each maps. Maps that are listed at games before RotE should be copied from RotE and placed to GR. That mistake is from 2005 Gold 4 CD North America edition. Most maps are placed to RotE and there is only 16 maps in GR Export.
Current GOG build already have own GOG DXCFG tool. That be better than wrapper-mod from Verok, because GOG wrapper - just wrapper. Verok did mod. It better for new experience. ach version of his mod have own featurs\-bugs.
Eg color pallete if wrong and cannot be restored in current versions. Although some previous build allow to disable this features compeltely. Now even for default colors game colors are wrong.
Very latest build of DisciplesGL should be fix also previously present in verok's wrapper bug - potions cannot be used on units itself - only to units cards. Widescreen battles bug.
GOG wrapper did the job to make game work as it should be and look a little bit better on current displays.Ofc no widescreen support. Veroks wrappers at least can zoom image to make it non-true widescreen. But again, DisciplesGL is more than just wrapper but mod.
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One of the manuals - d2_gold_manual is not include in game itself and only present in Downloadable goodies manuals archive.