fix: isolate think scratchpads by conversation

docs/tools/think/index.md

@@ -13,7 +13,7 @@ _Step-by-step reasoning scratchpad for planning and decision-making._
 
 The think tool is a reasoning scratchpad that lets agents think step-by-step before acting. The agent can write its thoughts without producing visible output to the user — ideal for planning complex tasks, breaking down problems, and reasoning through multi-step solutions.
 
-This is a lightweight tool with no side effects. It is most useful for models that lack built-in reasoning or thinking capabilities (e.g., smaller or older models). For models that already support native thinking — such as Claude with extended thinking, OpenAI o-series, or Gemini with a thinking budget — this tool is unnecessary since the model can reason internally.
+This lightweight tool changes only its internal scratchpad, not external data. It is most useful for models that lack built-in reasoning or thinking capabilities (e.g., smaller or older models). For models that already support native thinking — such as Claude with extended thinking, OpenAI o-series, or Gemini with a thinking budget — this tool is unnecessary since the model can reason internally.
 
 ## Configuration
 
@@ -28,3 +28,31 @@ No configuration options.
 > **When to use**
 >
 > Use the think tool with models that don't have native reasoning capabilities. If your model already supports a [thinking budget](../../configuration/models/index.md#thinking-budget), you likely don't need this tool.
+
+## Scope and lifetime
+
+Thoughts are isolated by conversation ID, calling agent and think toolset instance.
+They accumulate across turns, runtime closure and compaction. The built-in SQLite
+session store retains raw thoughts across reloads and restarts; the in-memory
+store retains them only for its lifetime. This internal state is stored before
+response-output redaction, so session-database and backup privacy policies apply.
+
+A branch or fork with a new conversation ID starts empty. A same-ID session clone
+addresses the same durable scratchpad; cloning messages does not provide a
+transactional copy of hidden thoughts. JSON export/import does not transport the
+scratchpad, and existing conversations start with empty dedicated state on upgrade.
+
+Toolset namespaces follow configuration order (configured and extra toolsets are
+separate). Resuming with reordered toolsets or another configuration with the same
+agent name can reassign these namespaces. Stable identity requires unchanged topology.
+
+Root deletion removes all root-owned thoughts, including those from aborted
+sub-sessions. Deleting a persisted child removes known subtree thoughts;
+never-persisted descendants remain root-owned until root deletion. Stop writers
+before deleting sessions. Deletion is logical, not secure erasure or backup removal.
+
+There is no TTL, eviction, quota or output omission: every call returns the full
+scratchpad, which can grow beyond model context limits. Storage and output memory
+scale with retained thoughts. Persistence, ownership or unsupported-store failures
+are tool errors, never silent resets. Only genuinely unscoped hosts, such as
+pre-run prompt expansion, return an ephemeral single thought.

pkg/runtime/loop.go

@@ -283,20 +283,23 @@ func (r *LocalRuntime) runStream(ctx context.Context, sess *session.Session, idl
 	// the whole lifetime of its stream.
 	entry := r.registerLiveSessionWithIdleRetry(sess, idleRetryPolicy)
 
+	// Persist the root before tools can append root-owned state.
+	out := r.observe(ctx, sess, events)
 	go func() {
 		if rootStream {
 			defer r.activeRootStreams.Add(-1)
 		}
 		r.runStreamLoop(ctx, sess, entry, events)
 	}()
-	return r.observe(ctx, sess, events)
+	return out
 }
 
 // runStreamLoop is the body of RunStream. Pulled out of the anonymous
 // goroutine so it has a real name in stack traces and is easier to navigate
 // in editors.
 func (r *LocalRuntime) runStreamLoop(ctx context.Context, sess *session.Session, liveEntry *liveSessionEntry, events chan Event) {
 	sink := &channelSink{ch: events}
+	ctx = context.WithValue(ctx, scratchpadRootKey{}, liveEntry.treeRootID)
 
 	// Seed the cagent session ID at the run-loop boundary so any
 	// gateway-bound HTTP call originating from this loop can correlate