ci/package_checks: Run package version checks against commits

[silkeh]

Summary

Update the PackageBumped check to check each commit individually, and check the untracked/modified files separately.

Resolves #5900

Test Plan

Ran locally against #5881. It now finds:

WRN packages/d/dotnet/package.yml:1: Package release is not incremented by 1 (ref: dc4f4a2d97b65beafde2016fe572f983318e3bfa)

Previously, it found:

WRN packages/d/dotnet-8/package.yml:1: Package release is not 1
ERR packages/d/dotnet-8/pspec_x86_64.xml:1: Package release is not 1
WRN packages/d/dotnet/package.yml:1: Package release is not incremented by 1
ERR packages/d/dotnet/pspec_x86_64.xml:1: Package release is not incremented by 1

Checklist

• Package was built and tested against unstable
• This change could gainfully be listed in the weekly sync notes once merged

[EbonJaeger]

LGTM, thanks!