chore(cli): remove dead --prune/-e flags from parseArgs

[pedrofrxncx]

The desktop link feature (the only consumer of --prune and -e/--env) was removed in #5570 ("chore(link): remove the desktop link feature"), but that PR left the two flag definitions dangling in apps/api/src/cli.ts's parseArgs options — they're accepted on the command line but never read anywhere (values.prune / values.env have zero references), and neither appears in the --help output.

A maintainer wants this because dead CLI flags are misleading: they silently accept --prune/-e <value> and do nothing, which is confusing for anyone poking at deco --help or grepping the source for what a flag does.

Net change: -5 lines, 0 added. Confirmed dead via grep -rn "values\.prune\|values\.env" apps/api/src/ (no hits) and by reading the git history of cli.ts back to the commit that introduced them for the link command.

A reviewer can confirm with:

grep -n "prune\|env: { type" apps/api/src/cli.ts

(no matches after this change) and cd apps/api && bunx tsc --noEmit.

Locally verified: bun run fmt, cd apps/api && bunx tsc --noEmit (clean), bunx oxlint src/cli.ts (0 warnings/errors). No test exercises these flags (there's no cli.test.ts), so this is a pure dead-code deletion — full CI validates the rest.

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Summary by cubic

Removes the unused CLI flags --prune and -e/--env from apps/api/src/cli.ts’s parseArgs. These flags belonged to the removed desktop link feature; they were previously accepted but no-ops and are now unrecognized to prevent confusion.

• Old vs new behavior: previously accepted and ignored; now not recognized. If your scripts pass these flags, remove them—there is no replacement.
• Review: only deletes the two option definitions (-5 lines). Verify with grep in cli.ts; typecheck remains clean.
• Help output is unchanged (these flags weren’t listed).

^{Written for commit 1e8b3b0. Summary will update on new commits.}