1.0: Correct agent guidance, help text, docs and legacy leftovers #1332

Goal: agent guidance, help, docs and test support match current behaviour.

• major: Agent guidance says a linked worktree does not use the main checkout's account. docs/agents.md:17-18, src/cmd/agent_notes.txt:24-25, src/cmd/agent.rs:83, plugin/bin/hook.py:26-63.
• major: agent --json leaves out the real --version flags. src/cmd/agent.rs:124.
• minor: architecture.md says ticket writes need push access. docs/architecture.md:13-16.
• minor: plan/migration.md lists working verbs as refused. plan/migration.md:20-28.
• minor: A plan/migration.md open item is already done. plan/migration.md:32-35.
• minor: The README leaves out repo create / edit / delete. README.md:109-123.
• minor: docs/output.md leaves out doctor setup's non-zero status. docs/output.md:171.
• minor: plan/output.md names removed types. plan/output.md:64-70.
• minor: plan/search.md points at a deleted file. plan/search.md:39.
• minor: api help promises a 404 hint. src/main.rs:214-215.
• minor: The agent briefing leaves out images and api. src/cmd/agent_notes.txt, src/main.rs:105-107.
• minor: completion help points at missing README steps. src/main.rs:154.
• minor: Dead legacy fixtures and PULL_STATUS_NSID. tests/fixtures/*, tests/support/mod.rs:75.
• minor: Source and test docs describe the old model and ATGC_USE_WEB. src/env.rs:3, src/cmd/mod.rs:10-15 and others.
• minor: Scripts and docs cite missing files. scripts/check-plan.py, lexicons/README.md, vendor scripts.
• minor: Stale NSIDs and scope list. Cargo.toml:160, vendor/tangled-lexicon/src/lib.rs:47-51, committed.toml:51-53.