fix(coding-agent): preserve run prompt during tool refresh

closes #6162

packages/coding-agent/src/core/agent-session.ts

@@ -21,6 +21,7 @@ import type {
 	AgentMessage,
 	AgentState,
 	AgentTool,
+	PrepareNextTurnContext,
 	ThinkingLevel,
 } from "@earendil-works/pi-agent-core";
 import type { AssistantMessage, ImageContent, Message, Model, TextContent } from "@earendil-works/pi-ai/compat";
@@ -331,6 +332,7 @@ export class AgentSession {
 	// Base system prompt (without extension appends) - used to apply fresh appends each turn
 	private _baseSystemPrompt = "";
 	private _baseSystemPromptOptions!: BuildSystemPromptOptions;
+	private _systemPromptOverride?: string;
 
 	constructor(config: AgentSessionConfig) {
 		this.agent = config.agent;
@@ -464,16 +466,20 @@ export class AgentSession {
 	}
 
 	private _installAgentNextTurnRefresh(): void {
-		const previousPrepareNextTurn = this.agent.prepareNextTurn;
-		this.agent.prepareNextTurn = async (turn, signal) => {
-			const previousSnapshot = await previousPrepareNextTurn?.(turn, signal);
+		const previousPrepareNextTurnWithContext =
+			this.agent.prepareNextTurnWithContext ??
+			(this.agent.prepareNextTurn
+				? async (_turn: PrepareNextTurnContext, signal?: AbortSignal) => await this.agent.prepareNextTurn?.(signal)
+				: undefined);
+		this.agent.prepareNextTurnWithContext = async (turn, signal) => {
+			const previousSnapshot = await previousPrepareNextTurnWithContext?.(turn, signal);
 			const previousContext = previousSnapshot?.context ?? turn.context;
 
 			return {
 				...previousSnapshot,
 				context: {
 					...previousContext,
-					systemPrompt: this.agent.state.systemPrompt,
+					systemPrompt: this._systemPromptOverride ?? this._baseSystemPrompt,
 					tools: this.agent.state.tools.slice(),
 				},
 				model: this.agent.state.model,
@@ -844,7 +850,7 @@ export class AgentSession {
 
 		// Rebuild base system prompt with new tool set
 		this._baseSystemPrompt = this._rebuildSystemPrompt(validToolNames);
-		this.agent.state.systemPrompt = this._baseSystemPrompt;
+		this.agent.state.systemPrompt = this._systemPromptOverride ?? this._baseSystemPrompt;
 	}
 
 	/** Whether compaction or branch summarization is currently running */
@@ -972,6 +978,7 @@ export class AgentSession {
 				await this.agent.continue();
 			}
 		} finally {
+			this._systemPromptOverride = undefined;
 			this._flushPendingBashMessages();
 		}
 	}
@@ -1143,10 +1150,12 @@ export class AgentSession {
 				}
 			}
 			// Apply extension-modified system prompt, or reset to base
-			if (result?.systemPrompt) {
+			if (result?.systemPrompt !== undefined) {
+				this._systemPromptOverride = result.systemPrompt;
 				this.agent.state.systemPrompt = result.systemPrompt;
 			} else {
 				// Ensure we're using the base prompt (in case previous turn had modifications)
+				this._systemPromptOverride = undefined;
 				this.agent.state.systemPrompt = this._baseSystemPrompt;
 			}
 		} catch (error) {