docs: reference/cli.md — one catalogue for every subcommand

[schubydoo]

Next split-epic chunk (REMEDIATION 3.2): the CLI was documented across five pages — a command list + headless blocks in installation.md, three reference sections inside operations.md's backup H2 (the audit's "four CLI references that aren't about backup"), api-token in public-api.md, and a README list missing seven headless commands entirely.

• docs/reference/cli.md — summary table + per-command sections. It is the full home for commands that only had scattered blocks (config reconcile, keepers, deps, the headless read/write commands, usage, the hash-* helpers, reap-environments — now documenting its real --archive / --force-delete flags), and a concise entry + canonical link for commands whose depth lives on a task page (doctor, backup/restore, api-token, install-service, mcp).
• operations.md — the config reconcile / keepers / deps sections move out; the backup H2 is about backup again; the intro points at the catalogue.
• installation.md — the subcommand catalogue collapses to a pointer (the pre-first-spawn doctor nudge stays).
• The moved deps text predated feat(deps): clauster deps install claustrum (Direct Session daemon) #984 and named only shawl; it now covers both pinned binaries (claustrum + shawl).
• README — the CLI list gains deps and the seven headless commands (projects/status/sessions/logs/open/start/stop) and links the page. Nav + llms.txt updated.
• Moved sections keep their exact old anchor slugs via explicit {#id} heading attrs — inbound links in glossary/troubleshooting/platforms/installation are repointed and the ids also satisfy markdownlint MD051 for the in-page table links (the spaced { #id } form does not; verified empirically).

Verification: every flag/verb/exit-code claim checked against __main__.py / deps.py / cli_write.py (independently re-verified by the docs-reviewer pass — no findings); full local gate green (4290 tests / 100% cov, lint-docs incl. MD051, strict mkdocs build with zero INFO link notices); all 14 anchors confirmed present in the built page.

🤖 Generated with Claude Code

[greptile-apps]

Greptile Summary

This PR consolidates the CLI documentation into one reference page. The main changes are:

• Adds a catalogue covering every CLI subcommand.
• Moves maintenance and headless command documentation from installation and operations pages.
• Updates README, navigation, cross-references, and llms.txt.
• Preserves old operations-page deep links with legacy fragment targets.

Confidence Score: 5/5

This looks safe to merge.

• The latest changes preserve all three moved operations-page fragments.
• Each legacy target is followed by a visible link to the new CLI catalogue.
• No blocking issues were found in the updated documentation paths.

Important Files Changed

Filename	Overview
docs/reference/cli.md	Adds the consolidated CLI catalogue with stable IDs for moved sections.
docs/operations.md	Replaces moved command sections with legacy fragment targets and a link to the new catalogue.
docs/installation.md	Replaces the scattered command list with a link to the CLI reference.
mkdocs.yml	Adds the CLI catalogue to the Reference navigation.

_{Reviews (2): Last reviewed commit: "docs: legacy anchor stubs for the moved ..." | Re-trigger Greptile}