diff --git a/packages/coding-agent/docs/session-tree.md b/packages/coding-agent/docs/session-tree.md
index 2564c422..839b23ca 100644
--- a/packages/coding-agent/docs/session-tree.md
+++ b/packages/coding-agent/docs/session-tree.md
@@ -16,16 +16,20 @@ Context is built by scanning linearly, applying compaction ranges.
 
 ## Proposed Format (Tree)
 
-Each entry has a `uuid` and `parentUuid` field (null for root):
+Each entry has a `uuid` and `parentUuid` field (null for root). Session header includes `version` for future migrations:
 
 ```jsonl
-{"type":"session","uuid":"a1b2c3","parentUuid":null,"id":"...","cwd":"..."}
+{"type":"session","version":2,"uuid":"a1b2c3","parentUuid":null,"id":"...","cwd":"..."}
 {"type":"message","uuid":"d4e5f6","parentUuid":"a1b2c3","message":{"role":"user",...}}
 {"type":"message","uuid":"g7h8i9","parentUuid":"d4e5f6","message":{"role":"assistant",...}}
 {"type":"message","uuid":"j0k1l2","parentUuid":"g7h8i9","message":{"role":"user",...}}
 {"type":"message","uuid":"m3n4o5","parentUuid":"j0k1l2","message":{"role":"assistant",...}}
 ```
 
+Version history:
+- **v1** (implicit): Linear format, no uuid/parentUuid
+- **v2**: Tree format with uuid/parentUuid
+
 The **last entry** is always the current leaf. Context = walk from leaf to root via `parentUuid`.
 
 Using UUIDs (like Claude Code does) instead of indices because:
@@ -312,33 +316,75 @@ With tree structure, could support:
 
 ## Migration
 
-### File Format
+### Strategy: Migrate on Load + Rewrite
 
-Add `uuid` and `parentUuid` fields to all entries. Existing sessions get generated UUIDs with linear parentage:
+When loading a session, check if migration is needed. If so, migrate in memory and rewrite the file. This is transparent to users and only happens once per session file.
 
 ```typescript
-function migrateSession(content: string): string {
-  const lines = content.trim().split('\n');
-  const uuids: string[] = [];
+const CURRENT_VERSION = 2;
+
+function loadSession(path: string): SessionEntry[] {
+  const content = readFileSync(path, 'utf8');
+  const entries = parseEntries(content);
   
-  return lines.map((line, i) => {
-    const entry = JSON.parse(line);
-    const uuid = generateUuid();
-    uuids.push(uuid);
-    entry.uuid = uuid;
-    entry.parentUuid = i === 0 ? null : uuids[i - 1];
-    return JSON.stringify(entry);
-  }).join('\n');
+  const header = entries.find(e => e.type === 'session');
+  const version = header?.version ?? 1;
+  
+  if (version < CURRENT_VERSION) {
+    migrateEntries(entries, version);
+    writeFileSync(path, entries.map(e => JSON.stringify(e)).join('\n') + '\n');
+  }
+  
+  return entries;
+}
+
+function migrateEntries(entries: SessionEntry[], fromVersion: number): void {
+  if (fromVersion < 2) {
+    // v1 → v2: Add uuid/parentUuid, convert firstKeptEntryIndex
+    const uuids: string[] = [];
+    
+    for (let i = 0; i < entries.length; i++) {
+      const entry = entries[i];
+      const uuid = generateUuid();
+      uuids.push(uuid);
+      
+      entry.uuid = uuid;
+      entry.parentUuid = i === 0 ? null : uuids[i - 1];
+      
+      // Update session header version
+      if (entry.type === 'session') {
+        entry.version = CURRENT_VERSION;
+      }
+      
+      // Convert compaction index to UUID
+      if (entry.type === 'compaction' && 'firstKeptEntryIndex' in entry) {
+        entry.firstKeptEntryUuid = uuids[entry.firstKeptEntryIndex];
+        delete entry.firstKeptEntryIndex;
+      }
+    }
+  }
+  
+  // Future migrations: if (fromVersion < 3) { ... }
 }
 ```
 
-Migrated sessions work exactly as before (linear path).
+### What Gets Migrated
+
+| v1 Field | v2 Field |
+|----------|----------|
+| (none) | `uuid` (generated) |
+| (none) | `parentUuid` (previous entry's uuid, null for root) |
+| (none on session) | `version: 2` |
+| `firstKeptEntryIndex` | `firstKeptEntryUuid` |
+
+Migrated sessions work exactly as before (linear path). Tree features become available.
 
 ### API Compatibility
 
 - `buildSessionContext()` returns same structure
 - `branch()` still works, just uses UUIDs
 - Existing hooks continue to work
+- Old sessions auto-migrate on first load
 
 ## Complexity Analysis
 
@@ -361,7 +407,7 @@ Abandoned branches remain in file but don't affect context building performance.
 ## Example: Full Session with Branching
 
 ```jsonl
-{"type":"session","uuid":"ses1","parentUuid":null,"id":"abc","cwd":"/project"}
+{"type":"session","version":2,"uuid":"ses1","parentUuid":null,"id":"abc","cwd":"/project"}
 {"type":"message","uuid":"m1","parentUuid":"ses1","message":{"role":"user","content":"Build a CLI"}}
 {"type":"message","uuid":"m2","parentUuid":"m1","message":{"role":"assistant","content":"I'll create..."}}
 {"type":"message","uuid":"m3","parentUuid":"m2","message":{"role":"user","content":"Add --verbose flag"}}