skills staleness notice still writes to stderr under --format markdown

[wmadden-electric]

#260 introduced --format markdown with the contract that everything lands on stdout and the engine writes nothing to stderr.

The skills staleness check in packages/cli/src/skills-check.ts runs outside the engine and writes its one-line notice straight to runtime.stderr. Its suppression list (shouldSkip, around line 160) exempts --json, --quiet, -q, --version, --format json, and --format=json, but not --format markdown / --format=markdown. So an agent that asks for markdown after a package upgrade still gets a line on stderr.

Two possible fixes:

1. Treat --format markdown like --format json in the suppression list. Simplest, but the notice is aimed at agents, and markdown is the format agents ask for, so this hides it from exactly its audience.
2. Under markdown, print the notice on stdout as part of the document (a trailing bullet, or a ### Diagnostics entry), and keep stderr empty.

The docs page for skills (prisma/web, apps/docs/content/docs/cli/skills.mdx, "The staleness check") lists the suppressing flags and currently matches the code, so it will need the same update once this is decided.

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