build: fix pre-commit hook for symlinked self-dep and staged deletions

[ochafik]

Summary

Two small pre-commit hook fixes split out of #620 / #530 where they were blocking commits:

• scripts/link-self.mjs: skip when node_modules/@modelcontextprotocol/ext-apps is a symlink (e.g. to the repo root). cpSync("dist", target/dist) was failing with ERR_FS_CP_EINVAL because src and dest resolved to the same path.
• .husky/pre-commit: capture staged files with --diff-filter=d so the xargs git add re-stage step doesn't fail with fatal: pathspec ... did not match any files on commits (typically merges) that include deletions.

Test plan

• npm run build:all completes with node_modules/@modelcontextprotocol/ext-apps -> ../.. symlink in place.
• Merge commit with deletions (examples/pdf-server/plugin/** removed) passes the hook.

[pkg-pr-new]

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commit: 6416f97