Extract runtime resource loader

[HabibPro1999]

What

• Extract a reusable coding-agent runtime resource loader.
• Move current resource discovery/loading responsibilities behind the loader without changing behavior.
• Preserve existing SDK/session setup semantics and extension/plugin discovery behavior.
• Add/update tests around skills, session isolation, tool activation, MCP discovery, model selection, and extension discovery.

Why

This creates the foundation for Pi-style runtime resource reloads and a future /reload command, while keeping this PR as a behavior-preserving internal refactor.

Part of the Pi runtime/agentic harness migration stack.

Testing

• bun test packages/coding-agent/test/sdk-skills.test.ts packages/coding-agent/test/sdk-session-isolation.test.ts packages/coding-agent/test/sdk-tool-activation.test.ts packages/coding-agent/test/sdk-mcp-discovery.test.ts packages/coding-agent/test/sdk-model-selection.test.ts packages/coding-agent/test/extensions-discovery.test.ts packages/coding-agent/test/plugin-extensions-discovery.test.ts packages/coding-agent/test/plugin-command.test.ts
• bunx biome check on all files changed by this PR
• Earlier pre-rebase checks: bun run check:ts and PATH="$HOME/.cargo/bin:$PATH" bun run check

Known caveat after rebasing onto latest main: full bun run check:ts is currently blocked by unrelated Biome formatting/import-order issues already present in origin/main files not touched by this PR (line-hash.ts, tools/renderers.ts, tools.test.ts, tools/search-renderer.test.ts).

---

• bun check passes (blocked after latest main rebase by unrelated upstream Biome issues listed above)
• Tested locally
• CHANGELOG updated (if user-facing; not required here because this is behavior-preserving internal refactor)