What happened?

Gemini CLI silently discards thoughtSignature in non functionCall parts on Gemini 3 responses in the in-memory chat history pipeline. Because the loss happens before this.history.push(), every multi-turn conversation is affected from turn 2 onward — checkpoint save/load is just the most visible symptom.

1. isValidContent rejects the signature-carrier chunk

packages/core/src/core/geminiChat.ts:

if (!part.thought && part.text !== undefined && part.text === '') {
  return false;   // ← also rejects { text: "", thoughtSignature: "..." }
}

The Gemini API docs explicitly describe this pattern (Thought signatures):

"During a model response not containing a FC with a streaming request, the model may return the thought signature in a part with an empty text content part."

So this gate silently drops the carrier chunk before it enters the history pipeline.

2. Consolidation loop drops thoughtSignature on merge

packages/core/src/core/geminiChat.ts, processStreamResponse:

if (lastPart?.text && isValidNonThoughtTextPart(lastPart) && isValidNonThoughtTextPart(part)) {
  lastPart.text += part.text;   // ← signature on `part` discarded
}

Even if (1) is fixed so the carrier enters modelResponseParts, this loop absorbs its empty text into lastPart and discards the signature (isValidNonThoughtTextPart doesn't look at thoughtSignature).

Empirical evidence

Raw stream probe via google-genai SDK against gemini-3-flash-preview, includeThoughts: true, thinkingLevel: HIGH:

• 34 chunks; signature appears only once — on the final chunk, exactly as the docs describe: { text: "", thoughtSignature_len: 2233, finish_reason: STOP }

After applying the 2-edit fix below in my fork and running a real conversation with /chat save:

• Before: { "role": "model", "parts": [{ "text": "<reply>" }] } — no signature anywhere
• After: { "role": "model", "parts": [{ "text": "<reply>", "thoughtSignature": "<~2KB base64>" }] } — a real signature (not the SYNTHETIC_THOUGHT_SIGNATURE placeholder that ensureActiveLoopHasThoughtSignatures injects)

Scope

Loss happens in this.history, not at save time. Affected:

• TUI chats, non-interactive gemini -p chains, agent loops, ACP sessions (--acp)
• Every multi-turn turn from the 2nd onward (lossy context re-sent to API)
• Checkpoint is only the most inspectable symptom — the underlying reasoning-continuity loss is universal

Because the API treats text-part thoughtSignature as OPTIONAL (Recommended), missing signatures don't cause 400 errors → silent quality degradation, not loud failure. This is likely why the bug has persisted.

What did you expect to happen?

thoughtSignature on text parts should be preserved in chat history (and by extension in checkpoints), so subsequent requests can echo them back and the model can resume reasoning state — as recommended by the official Gemini API docs.

Client information

CLI Version    0.38.2
Git Commit     b0ed611a0
Model          Auto (Gemini 3)
Sandbox        no sandbox
OS             linux
Auth Method    Signed in with Google
Tier           Gemini Code Assist in Google One AI Ultra

Login information

OAuth (personal Google account).

Anything else we need to know?

Minimal 2-edit fix (on top of v0.38.2):

--- a/packages/core/src/core/geminiChat.ts
+++ b/packages/core/src/core/geminiChat.ts
@@ -129,7 +129,7 @@ function isValidContent(content: Content): boolean {
     if (part === undefined || Object.keys(part).length === 0) {
       return false;
     }
-    if (!part.thought && part.text !== undefined && part.text === '') {
+    if (!part.thought && !part.thoughtSignature && part.text === '') {
       return false;
     }
   }
@@ -970,6 +970,9 @@ export class GeminiChat {
         isValidNonThoughtTextPart(part)
       ) {
         lastPart.text += part.text;
+        if (part.thoughtSignature) {
+          lastPart.thoughtSignature = part.thoughtSignature;
+        }
       } else {
         consolidatedParts.push(part);
       }