docs(v0.5.4): rewrite commands.md as a structured reference
Bring docs/commands.md up to current state. The document was last substantively updated in v0.5; v0.5.2 (restore/notes/path/list --names/ completion + archived-inclusive lookup), v0.5.3 (attach + --direct + persistent session mode + doctor tmux check), and v0.5.4 (info Session block + list SESSION column) were all undocumented. Format follows the spec section §3: each command has Purpose, Usage, Scenarios, Examples, Flags, Notes, Related. Sections are kept short (roughly one screen each) — if a command needed more, the command is doing too much, not the docs. New non-command sections: workspace layout (task and project), a consolidated environment-variables table (previously scattered), explicit query-resolution rules including archive-inclusive lookup behavior, session modes (direct vs persistent), and a shell-completion how-to. Examples use the canonical "ctask" command name per spec §3 — docs describe the product, not the user's local binary path.
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