diff --git a/packages/coding-agent/src/core/agent-session.ts b/packages/coding-agent/src/core/agent-session.ts
index 2db04ad4..f3c213d8 100644
--- a/packages/coding-agent/src/core/agent-session.ts
+++ b/packages/coding-agent/src/core/agent-session.ts
@@ -1704,7 +1704,7 @@ export class AgentSession {
 		let summaryEntry: BranchSummaryEntry | undefined;
 		if (summaryText) {
 			// Create summary at target position (can be null for root)
-			const summaryId = this.sessionManager.branchWithSummary(newLeafId, summaryText, summaryDetails);
+			const summaryId = this.sessionManager.branchWithSummary(newLeafId, summaryText, summaryDetails, fromHook);
 			summaryEntry = this.sessionManager.getEntry(summaryId) as BranchSummaryEntry;
 		} else if (newLeafId === null) {
 			// No summary, navigating to root - reset leaf
diff --git a/packages/coding-agent/src/core/compaction/branch-summarization.ts b/packages/coding-agent/src/core/compaction/branch-summarization.ts
index 132fd2ec..3647afb8 100644
--- a/packages/coding-agent/src/core/compaction/branch-summarization.ts
+++ b/packages/coding-agent/src/core/compaction/branch-summarization.ts
@@ -215,8 +215,9 @@ export function prepareBranchEntries(entries: SessionEntry[], tokenBudget: numbe
 
 	// First pass: collect file ops from ALL entries (even if they don't fit in token budget)
 	// This ensures we capture cumulative file tracking from nested branch summaries
+	// Only extract from pi-generated summaries (fromHook !== true), not hook-generated ones
 	for (const entry of entries) {
-		if (entry.type === "branch_summary" && entry.details) {
+		if (entry.type === "branch_summary" && !entry.fromHook && entry.details) {
 			const details = entry.details as BranchSummaryDetails;
 			if (Array.isArray(details.readFiles)) {
 				for (const f of details.readFiles) fileOps.read.add(f);
diff --git a/packages/coding-agent/src/core/session-manager.ts b/packages/coding-agent/src/core/session-manager.ts
index f1adda2a..11e4a146 100644
--- a/packages/coding-agent/src/core/session-manager.ts
+++ b/packages/coding-agent/src/core/session-manager.ts
@@ -64,6 +64,8 @@ export interface CompactionEntry<T = unknown> extends SessionEntryBase {
 	tokensBefore: number;
 	/** Hook-specific data (e.g., ArtifactIndex, version markers for structured compaction) */
 	details?: T;
+	/** True if generated by a hook, undefined/false if pi-generated (backward compatible) */
+	fromHook?: boolean;
 }
 
 export interface BranchSummaryEntry<T = unknown> extends SessionEntryBase {
@@ -72,6 +74,8 @@ export interface BranchSummaryEntry<T = unknown> extends SessionEntryBase {
 	summary: string;
 	/** Hook-specific data (not sent to LLM) */
 	details?: T;
+	/** True if generated by a hook, false if pi-generated */
+	fromHook?: boolean;
 }
 
 /**
@@ -872,7 +876,7 @@ export class SessionManager {
 	 * Same as branch(), but also appends a branch_summary entry that captures
 	 * context from the abandoned conversation path.
 	 */
-	branchWithSummary(branchFromId: string | null, summary: string, details?: unknown): string {
+	branchWithSummary(branchFromId: string | null, summary: string, details?: unknown, fromHook?: boolean): string {
 		if (branchFromId !== null && !this.byId.has(branchFromId)) {
 			throw new Error(`Entry ${branchFromId} not found`);
 		}
@@ -885,6 +889,7 @@ export class SessionManager {
 			fromId: branchFromId ?? "root",
 			summary,
 			details,
+			fromHook,
 		};
 		this._appendEntry(entry);
 		return entry.id;