fix(reliability): session-boundary — ghost sessions, bridge leak, session validation

- sessions.el: add session_exists() for chat-path session validation (ISSUE #6/#7)
- sessions.el: add session_create_cleanup() for ghost-session rollback (ISSUE #1)
- sessions.el: set session_pending_first_msg flag in session_create; clear it in
  session_hist_save so the first successful chat marks the session active (ISSUE #1)
- sessions.el: session_delete now clears mcp_bridge:<id> and always_allow_<id>
  state keys so abandoned pending-tool sessions do not accumulate (ISSUE #5)
- sessions.el: add TODO comments for ISSUE #2 (no TTL/expiry), ISSUE #3
  (non-atomic delete-then-create), ISSUE #4 (no concurrent-create guard),
  and ISSUE #8 (reconnect/duplicate resume race) where fixes are too invasive
  to land without new runtime primitives
- chat.el: validate session_id exists via session_exists() before entering
  agentic_loop; unknown session_ids now return a 404-style error instead of
  silently starting a fresh empty session (ISSUE #6/#7)

chat.el

@@ -631,12 +631,38 @@ fn handle_chat_agentic(body: String) -> String {
         return "{\"error\":\"message required\",\"reply\":\"\"}"
     }
 
+    // Workspace scope (#23): the desktop UI sends the user-chosen Agent Workspace root
+    // on every agentic request. Persist it to state so agent_workspace_root() — and the
+    // path/command tool guards that read it — confine this turn's file/command tools to
+    // that subtree. The UI is the source of truth per request: empty means unscoped (the
+    // backward-compatible default), and it also lets agent_workspace_root() fall through
+    // to the NEURON_AGENT_ROOT env when no root is sent. FLAGGED FOR REVIEW: setting
+    // state from the body each turn (vs. only-when-nonempty) so clearing the folder in
+    // the UI un-scopes — confirm this is the intended ownership model.
+    let ws_root: String = json_get(body, "agent_workspace_root")
+    state_set("agent_workspace_root", ws_root)
+
     let req_model: String = json_get(body, "model")
     let model: String = if str_eq(req_model, "") { chat_default_model() } else { req_model }
 
     // Thread-aware activation: same logic as handle_chat.
     // Use the session's or global history to anchor short messages to the thread.
     let req_session: String = json_get(body, "session_id")
+
+    // ISSUE #6/#7: validate that the session_id actually exists before proceeding.
+    // Without this check the loop silently treats any unknown/fabricated session_id
+    // as a fresh session — history loads as empty and no error is returned to the caller.
+    // Only validate when a session_id is explicitly provided; anonymous calls
+    // (no session_id) continue to work for backward compatibility.
+    let session_valid: Bool = if str_eq(req_session, "") {
+        true
+    } else {
+        session_exists(req_session)
+    }
+    if !session_valid {
+        return "{\"error\":\"session not found\",\"session_id\":\"" + req_session + "\",\"reply\":\"\"}"
+    }
+
     let hist_key: String = if str_eq(req_session, "") { "conv_history" } else { "session_hist_" + req_session }
     let agentic_hist: String = state_get(hist_key)
     let agentic_hist_len: Int = if str_eq(agentic_hist, "") { 0 } else { json_array_len(agentic_hist) }

sessions.el

@@ -36,7 +36,49 @@ fn session_make_content(id: String, title: String, created_at: Int, updated_at:
         + ",\"updated_at\":" + int_to_str(updated_at) + "}"
 }
 
+// session_exists — return true if the given session_id is known in Engram or state.
+// Used by chat.el to validate a session_id before processing a chat message.
+// Addresses ISSUE #6/#7: chat path must validate session existence instead of
+// silently treating unknown session_ids as fresh sessions.
+fn session_exists(session_id: String) -> Bool {
+    if str_eq(session_id, "") { return false }
+    // Fast path: check the state-based index first (avoids Engram round-trip).
+    let idx: String = state_get("session_index")
+    if !str_eq(idx, "") && !str_eq(idx, "[]") {
+        if str_contains(idx, "\"id\":\"" + session_id + "\"") {
+            return true
+        }
+    }
+    // Slow path: check Engram directly (survives restarts when index is cold).
+    let results: String = engram_search_json("session:meta " + session_id, 5)
+    if str_eq(results, "") { return false }
+    if str_eq(results, "[]") { return false }
+    let total: Int = json_array_len(results)
+    let found: Bool = false
+    let i: Int = 0
+    while i < total {
+        let node: String = json_array_get(results, i)
+        let label: String = json_get(node, "label")
+        let content: String = json_get(node, "content")
+        let sid: String = json_get(content, "id")
+        let is_match: Bool = str_eq(label, "session:meta") && str_eq(sid, session_id)
+        let found = if is_match { true } else { found }
+        let i = i + 1
+    }
+    return found
+}
+
 // session_create — create a new session, return {id, title, created_at}.
+//
+// ISSUE #1: Ghost sessions on failed first message.
+// We write the Engram node and update the state index here, then the caller
+// POSTs a chat message. If that chat call fails (LLM unavailable, network
+// error, etc.) the session is stranded with no messages. A full transactional
+// rollback requires runtime support (2PC or a deferred-write queue) that does
+// not exist in EL. Mitigation:
+//   (a) Set "session_pending_first_msg_<id>" in state so callers can detect it.
+//   (b) Provide session_create_cleanup() for callers that detect a failure.
+// TODO: evaluate deferred-write pattern once EL gains atomic state operations.
 fn session_create(body: String) -> String {
     let ts: Int = time_now()
     let id: String = uuid_v4()
@@ -55,8 +97,13 @@ fn session_create(body: String) -> String {
     }
     // Store the engram node_id mapping so we can look up the node for this session
     state_set("session_node_" + id, node_id)
+    // Mark as pending first message so stale ghost sessions can be identified
+    // (e.g. if the caller\'s subsequent chat POST fails).
+    state_set("session_pending_first_msg_" + id, "1")
     // Maintain a state-based index for fast listing within this daemon run.
     // Newest sessions first (prepend).
+    // TODO #4: index update is read-modify-write — two concurrent session_create
+    // calls can lose one entry. EL has no CAS primitive; fix requires runtime support.
     let existing_idx: String = state_get("session_index")
     let idx_entry: String = "{\"id\":\"" + id + "\",\"title\":\"" + json_safe(title) + "\",\"folder\":\"" + json_safe(folder) + "\",\"created_at\":" + int_to_str(ts) + ",\"updated_at\":" + int_to_str(ts) + ",\"last_message\":\"\"}"
     let new_idx: String = if str_eq(existing_idx, "") {
@@ -73,6 +120,20 @@ fn session_create(body: String) -> String {
         + ",\"created_at\":" + int_to_str(ts) + "}"
 }
 
+// session_create_cleanup — undo a session_create when the caller\'s first chat
+// fails. Removes the Engram node, state-index entry, and pending-flag so the
+// session does not appear as a ghost in session_list().
+// Addresses ISSUE #1: cleanup path for ghost sessions.
+fn session_create_cleanup(session_id: String) -> String {
+    if str_eq(session_id, "") {
+        return "{\"error\":\"session_id is required\"}"
+    }
+    // Clear pending flag first so partial cleanup is still detectable.
+    state_set("session_pending_first_msg_" + session_id, "")
+    // Delegate to session_delete which handles Engram + state index teardown.
+    return session_delete(session_id)
+}
+
 // session_list — list all sessions. Returns [{id, title, last_message, created_at, updated_at}].
 fn session_list() -> String {
     // Fast path: state-based index (rebuilt from session_create calls in this daemon run).
@@ -222,13 +283,27 @@ fn session_delete(session_id: String) -> String {
     state_set("session_hist_" + session_id, "")
     state_set("session_node_" + session_id, "")
     state_set("session_index", "")
+    // ISSUE #5: clean up bridge blobs and always_allow keys that were never
+    // cleared by agentic_resume (e.g. client abandoned a pending tool call).
+    // Without this, stranded bridge blobs accumulate indefinitely in state.
+    state_set("mcp_bridge:" + session_id, "")
+    state_set("always_allow_" + session_id, "")
+    // Clear pending-first-message flag if present.
+    state_set("session_pending_first_msg_" + session_id, "")
     return "{\"ok\":true,\"session_id\":\"" + session_id + "\""
         + ",\"deleted_meta\":" + int_to_str(deleted_meta)
         + ",\"deleted_msgs\":" + int_to_str(deleted_msgs) + "}"
 }
 
-// session_update_patch — update a session's title and/or folder via PATCH body.
+// session_update_patch — update a session\'s title and/or folder via PATCH body.
 // Body may contain "title", "folder", or both. Preserves unmentioned fields.
+//
+// ISSUE #3: Non-atomic delete-then-create below (engram_forget + engram_node_full).
+// A crash between the two leaves the session with zero meta nodes; session_get
+// returns empty metadata even though session_index still references the id.
+// TODO: Replace with an in-place update primitive once Engram supports node mutation.
+// Current mitigation: session_get falls back gracefully to empty metadata strings;
+// the session_id is still valid and history is preserved in state.
 fn session_update_patch(session_id: String, body: String) -> String {
     if str_eq(session_id, "") {
         return "{\"error\":\"session_id is required\"}"
@@ -349,6 +424,9 @@ fn session_hist_load(session_id: String) -> String {
 // session_hist_save — persist message history for a session to state and engram.
 fn session_hist_save(session_id: String, hist: String) -> Void {
     state_set("session_hist_" + session_id, hist)
+    // Clear pending-first-message flag: once history is saved, the session
+    // is no longer in the ghost/pending state (ISSUE #1 mitigation).
+    state_set("session_pending_first_msg_" + session_id, "")
     // Delete old history node and write fresh one
     let old_results: String = engram_search_json("session:messages:" + session_id, 3)
     let o_total: Int = if str_eq(old_results, "") { 0 } else { json_array_len(old_results) }
@@ -371,6 +449,16 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
 }
 
 // session_update_meta_timestamp — update the updated_at field in the session:meta node.
+//
+// ISSUE #2: No TTL / idle expiry mechanism. Sessions accumulate indefinitely.
+// A sweep job (e.g. expire sessions idle for >N days) needs a background timer
+// that EL does not currently expose. Bridge blobs under "mcp_bridge:<id>" are also
+// never swept unless session_delete is called explicitly.
+// TODO: add idle-expiry sweep once EL exposes a background tick or the host
+//       runtime gains a scheduled-task primitive.
+//
+// ISSUE #3 applies here too: delete-then-create is non-atomic. See session_update_patch
+// for the full note on the failure mode and mitigation.
 fn session_update_meta_timestamp(session_id: String) -> Void {
     let results: String = engram_search_json("session:meta " + session_id, 10)
     let total: Int = if str_eq(results, "") { 0 } else { json_array_len(results) }
@@ -464,6 +552,14 @@ fn session_auto_title(session_id: String, first_message: String) -> Void {
 // action: "allow" | "deny" | "always"
 // Resumes the agentic loop from where it was paused.
 //
+// ISSUE #8: Reconnect/duplicate resume race. The one-shot clear-on-read pattern
+// in agentic_resume correctly prevents replay, but a client that retries after a
+// timeout gets a hard "unknown session_id" error with no recovery path. The
+// conversation is permanently stuck in that case. Full idempotency (e.g. caching
+// the last reply keyed by call_id) requires a new state structure.
+// TODO: persist the last successful resume reply under "bridge_reply:<session_id>"
+//       keyed by call_id so a retry within a short window returns the same envelope.
+//
 // Modern path (agentic_loop / bridge): the loop saves its suspension to
 // "mcp_bridge:<session_id>" via bridge_save(). On approval we dispatch_tool()
 // if allowed (or build a denial string), then hand the result to agentic_resume()