test: add shallow & partial user-clone coverage (C5, C6)

Cover the two clone shapes a user can arrive with, across both checkpoint backends:

• C5: a git clone --depth=1 user clone runs the full session -> commit -> real-hook push -> read flow, and the checkpoint machinery never makes the repo shallower than git left it (no self-inflicted .git/shallow; regressions #1443/#1276). Reading the checkpoint tolerates the shallow boundary instead of corrupting it.
• C6: a git clone --filter=blob:none user clone reading a remote-only checkpoint lazily fetches the omitted metadata blobs, and the CLI stamps no new promisor/partialclonefilter config onto [remote "origin"] (regression #934). The .git/config guard enforces this at cleanup; an inline snapshot gives a clearer failure.

Refactors CloneFrom into cloneFromWithArgs so shallow/partial clone helpers can pass --depth/--filter over the smart file:// transport (required for those flags to be honored from a local bare).