docs: per-command and per-package guides under docs/{commands,packages}

[gmoigneu]

Summary

Adds two new doc subdirectories that mirror the runtime structure of gaal so a reader can navigate either by what they're trying to do (`commands/`) or by what they're trying to understand in the codebase (`packages/`).

`docs/commands/` — one page per CLI verb

`sync`, `status`, `info`, `init`, `audit`, `agents`, `doctor`, `migrate`, `schema`, `version` plus an index README. Each page covers:

• usage + flags
• exit codes (incl. `cmd.ExitCodeError` semantics)
• end-to-end execution flow as a `mermaid` flowchart (same style as issue meta: pre-launch full-codebase review — tracking issue + workflow diagrams #152)
• side effects: every path the command reads or writes
• links to the relevant package docs

`commands/sync.md` is the deepest write-up — covers planner-vs-apply, parallel repo fan-out, the skill-cache layout per OS, atomic install / merge / extract, snapshot writes, prune gating, service-mode failure cap, cancellation, and the tooling probe.

`docs/packages/` — one page per internal package

Includes the four support packages introduced by the recent reliability batch (`httpx`, `secfile`, `telemetry`, `tools`, `urlx`). Pages defer to the existing top-level pillar docs (`config.md`, `core.md`, `discover.md`) rather than duplicating them, and add:

• public-API tables
• dependency graphs
• recent-fix notes (PR / issue refs from the critical: os.Exit in sync/doctor bypasses PostRun (telemetry & consent flush skipped) #109-mcp: gate --prune behind per-target opt-in to avoid wiping manual entries #142 batch)
• runtime flow diagrams

Drift fixed in the existing top-level docs

`docs/architecture.md`:

• Adds `httpx`, `installscript`, `secfile`, `telemetry`, `tools`, `urlx` to the package tree and points at the new subdirs.
• Drops the stale `--yes` flag from the migrate row (PR fix(migrate): drop dead --yes flag #185 / migrate: --yes flag is declared but never used #141).
• Updates the repo-manager paragraph to reference the new package docs and vcs: VcsArchive.Update silently no-ops, freezing archive repos after first sync #124 for the archive-update tracking.

Pillars alignment

Reviewed the existing pillars and confirmed recent work doesn't add or change pillars:

• Config: 6 pillars (Config / Scope Policy / Schema / Validation / Platform / Template) intact.
• Core: 2 pillars (VCS / Agent Registry) intact.
• Discover: snapshot drift heuristic unchanged.

Recent PRs (#185-#207) are bug fixes / hardening within these pillars; package-level pages note them under "Recent fixes worth knowing".

Test plan

• All links resolve (`grep` audit)
• `go build ./...` and `go test ./...` pass (no code changed; sanity check)
• Manual render of the mermaid diagrams via GitHub Markdown preview