fix(mcp): shut down gracefully on stdin EOF instead of orphaning to PID 1 (#751)

[tobi]

Summary

• Reland of fix(mcp): shut down gracefully on stdin EOF instead of orphaning to PID 1 (#751) #767 onto current main (original was conflicted).
• Fixes qmd mcp (stdio) doesn't exit on stdin EOF — orphans to PID 1 and leaks RAM after parent dies #751: qmd mcp stdio shuts down on stdin EOF instead of orphaning to PID 1.
• CHANGELOG: kept Unreleased bullets and deduped duplicates from parallel merges.

Test plan

• test/mcp-stdio-lifecycle.test.ts green under Node 22 vitest (17) and bun (17)
• All test/mcp*.test.ts green under Node (67 passed / 14 skipped)
• Close fix(mcp): shut down gracefully on stdin EOF instead of orphaning to PID 1 (#751) #767 as superseded after merge