Bring the documentation back in line with how atgc behaves today. The fork route now shows the command that works: after repo fork --clone, pull commands take --remote upstream, and pr create and pr resubmit also name the fork. The agent notes and docs/agents.md say the same.
Elsewhere, issue view is described as reading Tangled's index with a knot fallback, the API examples list tickets from a knot rather than a PDS, and a blank issue body is sent as no body. The uninstall page lists the hook installers, the git identity and every file atgc leaves behind, including a second config directory. Output docs now describe notes, the missing-argument error, repo edit's changes array and base_changed, and name run watch --json beside doctor as printing an answer before a non-zero exit. Help text fixes cover the logs default, the run-list cap, repo view's nullable counts, the agent JSON keys, doctor local's push-access row, the reopen example, and the single-Tangled-remote fallback for --remote.
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