[Debugify] Strip added metadata in the -debugify-each pipeline

Summary:
Share logic to strip debugify metadata between the IR and MIR level
debugify passes. This makes it simpler to hunt for bugs by diffing IR
with vs. without -debugify-each turned on.

As a drive-by, fix an issue causing CallGraphNodes to become invalid
when a dead llvm.dbg.value prototype is deleted.

Reviewers: dsanders, aprantl

Subscribers: hiraditya, llvm-commits

Tags: #llvm

Differential Revision: https://reviews.llvm.org/D77915