fix(pkg): fix extra files with autolocking

[Alizter]

This patch makes sure we are using the internal lock directory rather than the source one. The previous code was traversing the lock directory source for the extra files and therefore autolocking, which directly produces the internal lock, would fail.

• fixes pkg: dune with pkg enabled fails to build an oxcaml project without a lock #12851

[punchagan]

Thanks for the clean up, alongside the bug fix!

[Alizter]

This change fixes a race condition with dev tools that triggers some other hidden bugs. I will factor those fixes out first and fix those issues, so marking this as draft in the meantime.

[Alizter]

Important technical notes about this patch:

When we copy a source lock directory to an internal one we are at the mercy of the interpreter of the pkg rules to read this lock directory correctly. At no point do we record the fact that there are extra files, we instead leave this to be inferred by the directory structure.

The previous implementation was inferring it directly from the source location which didn't work in every case, and left out autolocking.

Reviewed an earlier iteration of the code and is busy at the moment.

[shonfeder]

This looks great to me. Super clear. Thanks!