References: determine best place to wipe out a file's references

[mhanberg]

Description

If you save a file without actually changing the contents, the compiler won't compile the file again, but we are currently deleting all references from that file, in preparation for them to be replenished.

We should either delete the references when we know we are actually compiling, or conditionally delete them if we can determine if the file is actually dirty since the last save.

[mhanberg]

@dvic i have to mention you here so it'll let me assign you i think