feat(quickjs): remove built-in VFS globals, add PTC instance injection and StateBackend read-your-writes (#486)

### Summary
- Removed built-in readFile/writeFile globals from the QuickJS REPL.
File I/O is now exclusively through PTC tools, keeping the REPL a pure
JS sandbox with no implicit side effects
- ptc now accepts StructuredToolInterface instances directly alongside
tool name strings. Custom tools can be injected into the REPL without
being registered on the agent
- StateBackend now provides read-your-writes semantics within a single
js_eval superstep by reading via __pregel_read with fresh=true. Pregel
already tracks pending sends in task.writes; asking for a fresh read
applies them through the reducer, removing the need for a manual write
buffer
- Removed ptc: boolean shorthand from QuickJSMiddlewareOptions; use the
array or object forms instead

### Tests
- Added 12 unit tests to state.test.ts covering write-then-read, chained
edits, ls/grep/glob/readRaw visibility, upload/download, duplicate write
error, edit-nonexistent, and superstep boundary behavior
(commitSends/clearPending)
- Expanded middleware.test.ts with PTC instance injection coverage
- Verified end-to-end with createDeepAgent + createQuickJSMiddleware
across 7 scenarios (write-read, write-edit-read, write-ls, write-grep,
write-glob, cross-eval, upload-download); traces confirmed in LangSmith

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Co-authored-by: Hunter Lovell <40191806+hntrl@users.noreply.github.com>