Handle duplicated compile commands

[mcserep]

Compilation databases (compile_commands.json) may contain duplicated compilation commands for the same translation unit.

In such cases incremental parsing reports that the affected TU has already been parsed, even in case of a forced reparse. Clearly, incremental parsing was not prepared for such cases.

That issue should be fixed and it should be checked in general for the parser component of CodeCompass, that duplicated compilation commands are handled in an acceptable way.