Add Reference section for CLI commands

[cdebled]

Summary

• Add a new reference/cli/ section documenting each command's full option spec (agent, fetch, mcp, serve, run, version) plus shared common-options, sourced from the last version of help.zon
• Consolidate the four separate run-locally/commands/* usage guides into a single run-locally/commands.mdx page
• Slim usage/agent.mdx down to a practical guide, linking to the new reference for exhaustive option/REPL-command detail
• Update cross-links across the guide/usage pages to point at the new reference pages
• Add a ## help section to reference/cli/index.mdx (previously undocumented) and the missing /save REPL command row to reference/cli/agent.mdx
• Drop --cookie/--cookie-jar from reference/cli/mcp.mdx's own options block: help.zon duplicates them there (unlike .agent/.run), but they're identical to common-options.mdx, so the same dedup policy as fetch/serve applies

The option specs are copied verbatim from help.zon (the CLI's authoritative --help text). One deliberate exception: the real --help output for each command prints its own options followed by the common options in one combined block, but our docs split them — each command page shows only its own options, and the shared ones live once on common-options.mdx instead of being repeated on every command page.

This PR is part of a series splitting the new Reference section (CLI, MCP tools, HTTP API, PandaScript) into smaller pieces so each can be reviewed and merged on its own: #77 (MCP tools reference), #78 (PandaScript reference).

⚠️ To avoid live broken links, a few cross-references here temporarily point at the current usage guides instead of the reference pages another PR creates:

• reference/cli/mcp.mdx and run-locally/commands.mdx link to /usage/mcp#tools instead of /reference/mcp-tools; run-locally/commands.mdx also links to /usage/mcp#connecting-an-ai-agent, which Add Reference section for MCP tools #77 renames to #connect-an-ai-agent. Update all three once Add Reference section for MCP tools #77 merges.
• reference/cli/index.mdx and the new /save row in reference/cli/agent.mdx link to /usage/pandascript instead of /reference/pandascript. Update once Add Reference section for PandaScript #78 merges.

[arrufat]

Checked everything against browser main (f55aa1a66) and this one is fully up to date: every option block matches help.zon verbatim, including the newest flags (--block-urls, the mcp HTTP options, --save, the updated http defaults), and the REPL tables match SlashCommand.zig exactly, /stream and /searchEngine included. All new anchors resolve and no stale links to the deleted pages remain. Three small notes inline.

[arrufat]

Take it or leave it: these are the first fragment redirects, and the stub JS in generate-redirects.mjs does location.replace(href + location.hash), so an old bookmarked anchor like /run-locally/commands/serve#options lands on …/commands#serve#options. Probably fine to ignore, just flagging since the generator predates fragment targets.

[cdebled]

It requires just 1 line change in generate-redirect.js. Are you ok with this fix?
b455282:

docs/scripts/generate-redirects.mjs

Line 26 in b455282

<script>location.replace(${JSON.stringify(href)}${href.includes('#') ? '' : ' + location.hash'})</script>

[cdebled]

Heads up: #72 edits the four files this PR deletes/consolidates. It'll need to be closed once this merges.