make the whole projectContext still a reference after safeCloneDeep

[cderv]

projectContext should not be deep cloned. Only reference needs to be passed in the codebase.

This follows the works on

• Handle keep-ipynb correctly now that fileInformationCache is responsible for the cleaning #12793
• [backport] Fix regression with keep-ipynb  #12812

It happens that the whole projectContext object should not be cloned. Only reference to the created object should be passed throughout our codebase.

So a clone method is added as an identity function to work with our safeCloneDeep() logic.

This PR is quite simple but is there to check all our tests are passing.

This splits some changes from

• inspect - provide information about output files from input files #12809

and this PR is required to merge #12809

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