…enLM#3590, QwenLM#3505, QwenLM#3467) (#113)

* fix: backport upstream trivial bug fixes (QwenLM#3499, QwenLM#3630, QwenLM#3320)

Cherry-picked from QwenLM/qwen-code:

- QwenLM#3499 fix(core): use empty string instead of null for reasoning-only
  assistant content. Some OpenAI-compatible providers (e.g. Ollama
  qwen3.5:9b) reject content: null with HTTP 400 when reasoning_content is
  also present. Tool-call-only messages keep null per OpenAI spec.

- QwenLM#3630 fix(telemetry): switch FileExporter.serialize from JSON.stringify
  to safeJsonStringify. OTel ReadableSpans hold a BatchSpanProcessor
  back-reference that forms a cycle and crashed --telemetry-outfile users.

- QwenLM#3320 fix(core): cap chokidar depth at 2 in SkillManager and skip
  .git / special file types. Prevents FD exhaustion when a skill dir
  contains node_modules etc., which silently broke node-pty I/O.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(core): scope StreamingToolCallParser per-stream (QwenLM#3525)

Backports upstream PR QwenLM#3525 + extends the per-stream context to also
cover our fork's <think>-tag parser state.

Bug: every caller of Config.getContentGenerator() — foreground turns,
fork subagents, run_in_background subagents, ACP concurrent Agent calls
(after QwenLM#3463) — shared a single OpenAIContentConverter, which held the
StreamingToolCallParser as an instance field. Concurrent streams
corrupted each other's tool-call buffers, surfacing as NO_RESPONSE_TEXT.

Fix:
- New ConverterStreamContext interface holds toolCallParser, thinkBuffer,
  inThinkTag — one per stream.
- createStreamContext() factory replaces resetStreamingToolCalls().
- convertOpenAIChunkToGemini(chunk, ctx) and processThinkChunk(chunk, ctx)
  thread the context through every parser/think-buffer access.
- ContentGenerationPipeline.processStreamWithLogging creates one context
  at stream entry. The error path no longer manually resets — the
  context is GC'd when the generator unwinds.

Our protoInternal recovery-note logic is preserved on the new shape.

Note: upstream's follow-up QwenLM#3550 (full stateless converter refactor) is
deferred — it's hygiene without a functional bug; QwenLM#3525 alone fixes
the concurrency race.

Tests:
- New createStreamContext describe replaces resetStreamingToolCalls suite
- Streaming <think> tests use a per-test context
- pipeline.test.ts mock updated to match the new API
- pipeline.concurrent.test.ts (from upstream commit 38edd9d)
  drives two real concurrent streams and asserts neither corrupts the
  other's tool-call output (positive control: pre-fix, this test fails
  with exactly the user-reported bug shape).

Refs upstream QwenLM#3516, QwenLM#3525.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(core): strip thinking blocks from history on model switch (QwenLM#3304)

When switching models mid-session, reasoning_content fields from
thinking-capable models leaked into API requests sent to the new
provider, causing 422 errors on strict OpenAI-compatible endpoints.

Call stripThoughtsFromHistory() in handleModelChange() so thought parts
are removed before the next request is built for the new model.

* fix(core): reject truncated subagent write_file calls (QwenLM#3505)

Backport of upstream QwenLM#3505. Propagates MAX_TOKENS truncation from
subagent responses into tool requests and rejects truncated edit calls
before schema validation can surface misleading missing-parameter errors.

Adapted to our fork's coreToolScheduler.ts which already had the
truncation rejection block — kept both, dropped the unused
clearRetryCountsForTool() call (we don't have that retry-counter
machinery yet).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(core): prevent malformed permission rules from becoming tool-wide catch-alls (QwenLM#3467)

Backport of upstream QwenLM#3467. A permission rule with unbalanced parens
was silently parsed with specifier: undefined, causing matchesRule to
treat it as a catch-all. For deny rules this blocked all commands; for
allow rules a typo could silently auto-approve everything.

- Adds an invalid flag to PermissionRule
- parseRule marks unbalanced-paren rules as invalid
- matchesRule short-circuits invalid rules to never match
- parseRules / addSession*Rule / addPersistentRule warn on malformed input
- listRules filters invalid rules from /permissions UI

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(core): preserve reasoning_content during session resume and active sessions (GH#3579)

* test(config): drop fork-incompatible QwenLM#3304 strip-thoughts test

The test from upstream QwenLM#3304 backport assumed an in-place qwen-oauth
model switch path that our fork doesn't have; the source-side fix in
config.ts (stripThoughtsFromHistory call in handleModelChange) is
preserved. Coverage will be re-added when the fork's switch flow
stabilizes.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Automaker <automaker@localhost>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: tanzhenxin <tanzhenxing1987@gmail.com>
Co-authored-by: Yuchen Fu <fuyuchen0904@163.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…e sessions (GH#3579) (QwenLM#3590)

* fix(core): preserve reasoning_content during session resume and active sessions (GH#3579)

* chore(core): remove dead thinkingThresholdMinutes config after latch removal (GH#3579)