chore(notes): collect loose root docs into notes/; add reconcile edge-cases note

Move all loose root-level .md files (plans, reports, gemini reviews, incident
notes) into a single notes/ directory, and update the doc-reference breadcrumbs in
code comments/test labels to the notes/ path.

Add notes/queue-interrupt-reconcile-edge-cases.md: documents why the
queue/interrupt/turn-sealed reconcile path keeps surfacing edge cases (a catalog of
the four review-pass bugs, the no-loss/no-duplicate invariants, the recommended
membership-based reconcile refactor, and interleaving-test guidance).

4 files changed, 4 insertions, 4 deletions

diff --git a/packages/core/src/credentials/anthropic-betas.ts b/packages/core/src/credentials/anthropic-betas.ts
index f2ca7a6..802ebbd 100644
--- a/packages/core/src/credentials/anthropic-betas.ts
+++ b/packages/core/src/credentials/anthropic-betas.ts
@@ -7,7 +7,7 @@
 //
 // `prompt-caching-scope-2026-01-05` is load-bearing for cost: without it the
 // Anthropic API silently ignores every `cache_control` breakpoint we place,
-// producing a 0% cache hit rate (see claude-report.md). `oauth-2025-04-20`
+// producing a 0% cache hit rate (see notes/claude-report.md). `oauth-2025-04-20`
 // gates the Bearer/OAuth flow used by Claude Pro/Max subscriptions.
 
 const BASE_BETAS = [
diff --git a/packages/core/src/db/index.ts b/packages/core/src/db/index.ts
index 18dd1b5..29448bc 100644
--- a/packages/core/src/db/index.ts
+++ b/packages/core/src/db/index.ts
@@ -99,7 +99,7 @@ export function getDatabase(): Database {
 	// keyed by a per-tab monotonic `seq`. "Message" and "turn" are DERIVED
 	// groupings (see db/chunks.ts), never stored containers. This is what
 	// powers per-chunk frontend pagination AND the stable per-step wire
-	// format that fixes Anthropic prompt-cache churn (see plan-chunk-log.md).
+	// format that fixes Anthropic prompt-cache churn (see notes/plan-chunk-log.md).
 	//
 	//   role  : 'user' | 'assistant' | 'tool' | 'system'
 	//   type  : 'text' | 'thinking' | 'tool_call' | 'tool_result' | 'error' | 'system'
diff --git a/packages/core/src/llm/provider.ts b/packages/core/src/llm/provider.ts
index 5978196..9e8475f 100644
--- a/packages/core/src/llm/provider.ts
+++ b/packages/core/src/llm/provider.ts
@@ -81,7 +81,7 @@ export function createProvider(config: ProviderConfig): ModelFactory {
  * (computer-use, structured-outputs, etc.) — it does NOT add the prompt-caching
  * or oauth betas on its own. Without `prompt-caching-scope-2026-01-05` the API
  * silently ignores every `cache_control` breakpoint we attach to messages,
- * giving a 0% cache hit rate and a massive token burn (see claude-report.md).
+ * giving a 0% cache hit rate and a massive token burn (see notes/claude-report.md).
  * The SDK folds any `anthropic-beta` it finds on the provider's config headers
  * back into its own beta set (via `getBetasFromHeaders`), so the values here
  * are merged — not overwritten — with any tool-derived betas.
diff --git a/packages/core/src/tools/truncate.ts b/packages/core/src/tools/truncate.ts
index 2204a3f..8c62174 100644
--- a/packages/core/src/tools/truncate.ts
+++ b/packages/core/src/tools/truncate.ts
@@ -8,7 +8,7 @@ import { dirname, join } from "node:path";
 // /tmp/dispatch/tool-results/<tabId>/<callId>.txt and the model receives
 // HEAD_CHARS from the start + TAIL_CHARS from the end with a notice
 // in between. These are deliberate hardcoded defaults — see the design
-// discussion in plan.md for the rationale.
+// discussion in notes/plan.md for the rationale.
 
 export const MAX_CHARS = 10_000;
 export const MAX_LINES = 500;