fix(coding-agent): report custom queues and require extension code restarts

[fitchmultz]

Summary

• Fix ctx.hasPendingMessages() missing custom steering/follow-up messages because it checked the UI's user-text count. Extension contexts and interactive shortcuts now use Agent.hasQueuedMessages(). The UI count stays user-text-only; nextTurn and context-only asides remain excluded from the pending-work predicate.
• Reinitialize cached extension factories on fresh runtimes during /reload instead of clearing the factory cache. Settings and non-code resources still reload; discovery, extension path/enable-disable changes, and shutdown/start lifecycle handling remain intact.
• Require a full Pi process restart after changing extension code or dependencies. Clearing Pi's factory cache did not reliably refresh native module code. TUI/RPC reload notices, help, SDK docs, and the example now state the restart requirement; /new and session switching are not substitutes. No Jiti fork, dependency changes, or lockfile changes.

Validation

All results are for acf4c2d98ec44de2108f16a47bf59de5193341a7:

• macOS arm64, Node 24.20.0: npm run check and ./test.sh passed. Credential-dependent provider tests were intentionally skipped.
• Linux arm64, Node 24.19.0 and 22.19.0: isolated offline builds, checks, 148 targeted tests across 10 files, source/bundled CLI version/help, and real RPC reload/restart probes passed.
• Regressions cover custom queues retained after abort, clearQueue, excluded asides, cached factory reruns, JS/TS entrypoint/schema changes requiring restart, refreshed prompts, and TUI/RPC notices.
• Source, unbundled SDK, and bundled SDK probes retained old code/schema through reload and loaded updates after a fresh process. The bundled macOS TUI displayed the restart warning.

Full Linux suites, Linux x86-64/interactive TUI, real provider calls, Bun standalone binaries, and actual Node SEA binaries were not tested. The Node SEA loader configuration regression passed.

Compatibility

The package version remains 0.85.1; that version alone does not identify this behavior. The native revision boundary is acf4c2d98ec44de2108f16a47bf59de5193341a7. Companion pi-subagents changes will depend on this commit. After installing this revision, fully restart running Pi processes to acquire the native queue fix and updated extension code.