Have run.py utility correct for mismatches in compile_commands.json produced by BEAR rather than cmake

[secure-sw-dev-bot]

This issue was copied from checkedc/checkedc-clang#525

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compile_commands.json files produced by BEAR have a slightly different structure than those produced by cmake. Additionally, they use relative paths instead of absolute paths. This seems to be confusing checked-c-convert as it tries to find the compile commands. To fix it, let's have run.py modify BEAR-produced compile_commands.json files to match the formatting of cmake-produced files.