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Which mature version control systems allow overriding algorithms of finding and applying delta? Either through plugin or through exteral tool, does not matter.
It must be possible to override internal diff algorithm of a VCS for specific file types. Custom deltas must be stored in the repository to be used by the delta applying algorithm.
Internal binary diff is not acceptable in my case.
I mean exactly overriding algorithms, not displaying the differences using a custom diff program.
For Server Side:
As far as I know (I´m no expert on this subject!) this is not easily done. So you´re best shot seems to get the source from Apache Subversion and modify/extend it according to your needs. Taking a look into “Pre-Commit Hooks” is also an idea.
For Client Side:
ClearCase has some nice extra Merge Tools for e.g. office documents.
Also it is possible to change the diff/merge tool in the Tortoise SVN Client.