Allow Directory Comparison with Different Filters

[Luke]

With more developers using GIT or similar Version Control Systems, I have files and folders in my local folders which I must retain, but which I would not want/need to upload to my FTP server.

Similarly, some other developers (working on the same projects, or who have created plugins or other software which I am using) may have failed to properly sanitise their files, resulting in files being on the server which cannot be seen when I have a Filter applied, and which prevent the deletion of some folders (because the folders, containing these hidden files, are not empty).

Attempting to apply a Filter, where "CVS and SVN directories" are filtered locally (so I don't upload them) and not remotely (so I can see them and delete them as needed), when I try and apply Directory Comparison, I get an error:

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Directory comparison failed
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Cannot compare directories, different filters for local and remote directories are enabled
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OK   
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Could this alert be modified so that the buttons are "OK" and "Ignore"? Allowing users who want to apply different local and remote filters to do so, but warning other users that they may not be seeing a correct reflection of the local and remote files?