feat: Add clear orphans command

[jedijashwa]

Closes#236

Adds a semble clear orphans subcommand along the lines suggested in the issue: it walks the sha-named cache entries, reads root_path from each metadata.json, only considers entries whose dir name matches the cache key for the resolved root_path (which filters out git-URL entries), and removes the ones whose path no longer exists. Prints each cleared path, or "No orphaned indexes found".

I pulled the hashing out of find_index_from_cache_folder into a cache_key helper so the orphan check uses the same key computation instead of duplicating it. Ruff's complexity limit also made me split _run_clear into per-type helpers.

make test, make lint, and make typecheck all pass. Also tested end to end against my real cache: indexed a scratch dir, deleted it, ran semble clear orphans, and it removed just that entry and nothing else. A second run prints the no-orphans message.

[greptile-apps]

Confidence Score: 4/5

The PR is not yet safe to merge because malformed metadata can abort cleanup and temporarily unavailable sources can still lose their cached indexes.

The type-validation reply reports the metadata issue fixed, but calling .get() directly on decoded JSON leaves a concrete counterexample: a valid non-object document raises before the new root_path guard. The previously reported unavailable-source path also remains unchanged, with a failed existence check directly leading to cache deletion.

Files Needing Attention: src/semble/cli.py, tests/test_cli.py

_{Reviews (2): Last reviewed commit: "fix: Validate root_path type when cleari..." | Re-trigger Greptile}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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

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[Pringled]

@jedijashwa LGTM, thanks for contributing! We'll include this in the next release 😄