docs: fix Harmony CLI reference; flag real auto-apply bug (staging#93)
Discovered while researching Build With Muse Episode 09: the Harmony CLI reference table documented subcommands that don't exist at all -- 'muse harmony patterns', 'resolutions', 'policies' -- confirmed against the real 'muse harmony --help' subcommand list (list, show, best, record, resolve, forget, clear, gc, policy-add, policy-list, policy-remove, audit, engine, similar, escalate, escalations, resolve-escalation). Corrected every entry to real, verified syntax, including several with wrong flag names (--age-days -> --age) or wrong argument shapes entirely (the old 'engine <path> <ours-id> <theirs-id>' example bore no resemblance to the real 'engine PATTERN_ID' signature).
Also added an explicit warning on the idiomatic workflow's step 8: live testing confirmed (twice, from a clean repo) that harmony's auto-apply reports '[harmony] auto-resolved' and increments applied_count, but the merged file's actual content is 'ours' unchanged -- not the recorded resolution's outcome_blob. Filed as musehub staging#93. Flagging this directly in the doc so no future agent session trusts the checkmark alone before this is fixed.
Co-Authored-By: Claude Sonnet 5 <[email protected]>
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