feat: add clear command to clear indices

[stephantul]

This PR adds a semble clear command. clear takes a single argument: "all", "savings" or "index". "all" clears everything, "savings" clears the savings jsonl, "index" only clears saved indexes. Indexes are only cleared if they are complete, and all files are present.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
src/semble/cli.py	100.00% <100.00%> (ø)

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[greptile-apps]

Confidence Score: 4/5

Safe to merge; the deletion guards (SHA-256 regex + PersistencePath.non_existing()) prevent unintended data loss, and the change is purely additive.

The core logic is straightforward and well-protected. The two style issues (glob breadth and type shadowing the built-in) do not affect correctness. The gap in the index-deletion tests — where no assertion checks that the directories are actually gone from disk — leaves a small blind spot but does not indicate a current defect.

The index-clearing test cases in tests/test_cli.py would benefit from an on-disk existence check to match the rigour of the savings tests.

_{Reviews (1): Last reviewed commit: "feat: add clear command to clear indices" | Re-trigger Greptile}

[Pringled]

LGTM! Few small suggestions to reduce number of tests but not blocking