scripts: kconfig: normalize paths to avoid duplicate

There is a bug where non-normalized paths can introduce multiple entries
for the same file. E.g. '/1/2/../2.file' and '/1/2/3/../../2.file' would
both be listed, and end in a ninja error because multiple targets
generate the same file.

This commit fixes this issue by normalizing the paths.

Signed-off-by: Håkon Øye Amundsen <haakon.amundsen@nordicsemi.no>