Eclipse file search finds the same file multiple times

In an open resource window (cntrl+shift+R), click on the arrow on top-right and check "Filter Duplicated Resources". This worked for me.

What I personally do to avoid this is marking each module in the parent project as derived (right-click on the folder > properties > Attributes: Derived).

Then when you perform a file search, uncheck "Consider derived resources" (I don't think it is checked by default) and you won't get the A/B/<my_file>.

The only inconvenience is that you must do this for each module, and each time a new module is added.