fix(cli): resolve pnpm catalog: protocol references in CLI build output

[Swimburger]

Description

Refs: Reported by @Swimburger

The published @fern-api/fern-api-dev (and potentially fern-api) CLI packages had broken package.json files containing raw pnpm catalog: protocol references instead of resolved version numbers:

"dependencies": {
  "@boundaryml/baml": "catalog:"
}

Root cause: The CLI build scripts write catalog: specifiers from the source package.json into the output dist/*/package.json. The publish scripts then used npm publish, which does not understand pnpm's catalog: protocol — so the raw string was published verbatim instead of the resolved version (e.g. ^0.211.2).

Fix: Switch from npm publish to pnpm publish --no-git-checks. pnpm publish natively resolves catalog: references from pnpm-workspace.yaml at publish time. --no-git-checks is needed because the dist directory contains generated (uncommitted) build artifacts.

Link to Devin run

Changes Made

• Changed publish:cli:dev and publish:cli:prod scripts in packages/cli/cli/package.json from npm publish to pnpm publish --no-git-checks

Human Review Checklist

• Verify pnpm publish resolves catalog: for excluded directories: The dist/dev and dist/prod directories are explicitly excluded from the pnpm workspace in pnpm-workspace.yaml. Locally verified that pnpm pack does resolve catalog: → ^0.211.2 for a test package in this location, but worth confirming in CI.
• Flag passthrough from seed.yml: The publish commands in seed/fern-cli/seed.yml append flags like --access public --tag latest after the script name (e.g. pnpm --filter @fern-api/cli publish:cli:dev --access public --tag latest). Verify these flags are correctly forwarded to pnpm publish.
• cli-v2 not affected: cli-v2 does not have its own publish scripts in package.json, so no changes needed there.

Testing

• Manually verified that pnpm pack resolves catalog: → ^0.211.2 for a test package.json placed in the dist directory
• Full end-to-end publish not tested (would require npm credentials and a real publish)

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