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If the development team confirms this...(I haven't done this yet) but if they confirm this...this one has to be fixed ASAP. Manual aligning is a very important option to be able to use.
This is a limitation of manual align in BC3, not a bug. Manual align can only align files that are in the same subfolder relative to the base folders. This is true when folders aren't flattened, it is also true when folders are flattened.
In your screen cast, the file on the left is in the root of the base folder. On the right it is in a subfolder of the base folder. Because they are in different folders the current version of BC3 can't manually align them. If the files had different names but were in the same subfolder manual align would work.
Support for manually aligning files that are in different folders is on our wish list for a future release of BC.
Manual align can only align files that are in the same subfolder relative to the base folders. This is true when folders aren't flattened, it is also true when folders are flattened.
I would think that enabling manual align for files not in the same relative path when folders are flattened shouldn't be an unreasonable request considering the fact that BC3 already auto-aligned the file with a file not in the same relative path.
So long as the alignment does not require a re-ordering of the files on one side or the other, it should be supported... in my opinion.
BC v4.0.7 build 19761
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