fix(agent-runtime): keep tool-call ids unique in every request

[zhangqingkun976]

Toward #718. This does not claim to find the writer that duplicated the call — it makes the request valid when one exists, and it makes the next report name the writer.

Why this shape

@muzimu217's data-side check narrowed the 400 to the assembly path and listed three candidates (snapshot merging, the compaction boundary, retry replay). I verified what I could against the source and ruled two of them out:

• A tool row's id is its call id (apps/desktop/electron/main/runtime/event-persistence.ts:327, :334), and the host read is keep-last by id (crates/host-core/src/sessions.rs:752 dedupe_records, applied on both session.get paths). So the "same call, same row id" case is already collapsed — the surviving shape is one call under two different row ids, which nothing collapses.
• The compaction boundary does not reintroduce tool-call pairs: the DeepSeek-specific reasoning replay drops them (packages/agent-runtime/src/reasoning-replay.ts:109, "Tool-call blocks are dropped on purpose"), and the retained tail keeps user messages only.

I could not pin the writer without a DeepSeek key or the reporter's transcript, so the change is built to be correct either way:

A request can never carry a duplicate tool_use id. The guard runs in convertToLlm, the last view before the wire, which is the one place that sees both a rebuilt history and one that grew during this process:

• the first occurrence of an id keeps its call, and its result;
• a later call for that id, and a later result for it, are dropped — so the call/result pair the provider validates stays well-formed (dropping only the call would leave an orphan result, which is a different 400);
• a request with no duplicates is returned unchanged (the same array, not a copy), so the common path pays nothing;
• a drop writes one line to the agent log channel: [agent-runtime] dropped N duplicate tool call entries before the request (session=… ids=…).

That log line is the point of the exercise: the next session that hits the provider's sentence turns it into the answer instead of another hypothesis about which of the three candidates it was.

What it does not do

• It does not fix the writer. If a duplicate is a symptom of something re-persisting a row, that bug is still there — this only stops it from bricking a session, and now says when it happens.
• It does not rename ids (renaming would break the result pairing) and it rewrites nothing on disk.
• No compaction, retention, budget or transcript rule changes.

Validation

packages/agent-runtime/src/runtime.test.ts:

• duplicated transcript — a history carrying the same call under two row ids: the request view keeps one toolCall (call-1) and exactly one toolResult with the matching toolCallId, and logs one line naming the session and the id.
• unique transcript — the same helper returns the identical array and logs nothing.

Full suite: pnpm --filter @pi-desktop/agent-runtime test → 46/47 files; the one failure is the pre-existing native-pi-session case that fails identically on pristine main. pnpm --filter @pi-desktop/agent-runtime build 0; pnpm lint clean; node scripts/check-architecture.mjs passed; pnpm docs:check (78 EN/zh pairs, 495 pages) exit 0.

E2E gate: NOT RUN. The scenario is written (E2E-RUNTIME-unique-tool-call-ids-per-request, both locales, with traceability rows) but no desktop E2E suite was executed: it needs a deterministic provider fixture that captures the outgoing request, which this repository does not have yet. Alternative validation: the runtime-level tests above build a real runtime from a duplicated history and assert on the same view the request is built from. Remaining risk: the live-appended half of the guard (a duplicate that appears mid-session) is covered by the shared code path but not by a test that provokes it.

Docs

03-runtime/02-agent-runtime.md §5 (the restored-history bullets), 08-meta/decisions-log.md D608, and the E2E scenario above — all mirrored to docs/zh-CN/….

D608 is numbered after the D604–D607 proposed in my open #721, #748 and #756; I will renumber if those land first.

[vastsa]

I verified that the duplicate tool-call-id failure in #718 is real, but this PR does not repair the writer or message-assembly path. It only drops later duplicates in convertToLlm at the outgoing boundary; persisted or compacted history can still contain the duplicate IDs, and the PR explicitly leaves the writer unfixed. The PR also records its E2E gate as NOT RUN.

This is a downstream mitigation rather than a root-cause fix, so it is not safe to merge under the repository PR intake rules. I am closing this PR; issue #718 remains open.

[zhangqingkun976]

Rebased onto main (ab39a9b4) so the new Head contains latest base gate passes. Head is now 0d934d1f.

The only conflicts were append-vs-append — the E2E scenario catalog and the decisions log, where main and this branch each added an entry — and both sides are kept. The identifier bands are still free: upstream's newest ADR is 0299 and its newest decisions-log entry is D607 (the plugin crash report, which is this repository's own fix for issue #747 built on my #756).

[zhangqingkun976]

Closed by accident and GitHub will not reopen it: an API-side ref update to rebase the branch reads as a force-push, and reopening is blocked for such a branch. The same content continues in #780.