to now manually unravel the duplication by hand
This is a classic refactoring problem.
The amount of duplication doesn't matter, you simply go file by file, and re-write each file to be modular, using the appropriate amount of abstraction.
By the time you're on file 20 (of 500), you'll know if possible (and worth the effort ) to refactor all 55k lines of code, or start from scratch.
If this were perl, I would say use B::Xref to generate a graph, and then look for cycles ...
Or if the code is at all modular, use autodia and/or GraphViz::ISA to get a picture
surely php has something similar, maybe :)
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