projects: Separate output files based on target

[malmeloo]

One project can have multiple configured targets, but the output files will be thrown into the same file list. This may result in seemingly duplicate output file entries. It would be better to keep track of the target ID for each output file so that they can be separated.

Question: how do we handle changes to an existing target's architecture? Some files, such as rtl.yosys.json will overwrite previous output files if the target was different (since the file name is always the same), but others such as the Yosys synthesis output (<architecture>.json) will generate a new file under the same target directory. This could generate some confusion if we re-label the old output file as if it has the new architecture.