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I don't understand what the issue is. These flags where added in #558 to make the file paths in the debug sections relative to the compiler and project sources. The {gccpath} is computed by the build system, since it differs per OS/user.
modm/tools/build_script_generator/common.py
Lines 221 to 222 in ae85805
These flags are build system dependent and not filtered, will always create a useless one.
-ffile-prefix-map==.
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