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Marking as resolved; if anyone else is interested in the solution, this was fixed in the latest version of the code, I changed the algorithm that powers the hardening options, originally it was using the not-so-standard Apache 2.4 conditions to determine which module would process the access to certain files, when the hardening was applied to the includes directory two exceptions were added to the access control file to allow execution of the file manager and the visual editor, these exceptions were still using the old Apache 2.2 rules; the latest version of the code handles this situation better.