diff --git a/README.md b/README.md
index 64477e5..95f6971 100644
--- a/README.md
+++ b/README.md
@@ -63,11 +63,11 @@ ollie/
       systemprompt      read:  fully rendered system prompt for this session
       tail              exec:  exec tail -f chat
       usage             read:  token counts (input, output, requests; [estimated] if not reported by backend)
+      t/                dir:   tool scripts (r/w, backed by ~/.config/ollie/tools/)
+        idx             read:  tool index (name, description, args — synthesized at read time)
+        <script>        r/w:   tool script content
   sk/                   dir:   skills (r/w, from OLLIE_SKILLS_PATH or ~/.config/ollie/skills/)
     <name>.md           r/w:   skill SKILL.md content
-  t/                    dir:   tool scripts (r/w, backed by ~/.config/ollie/tools/)
-    idx                 read:  tool index (name, description, args — synthesized at read time)
-    <script>            r/w:   tool script content
   tr/                   dir:   saved transcripts (read, backed by OLLIE_TRANSCRIPT_PATH or ~/.config/ollie/transcript/)
     <timestamp>-chat.md read:  transcript saved at session end
   tmp/                  dir:   temporary files (r/w, backed by OLLIE_TMP_PATH or $XDG_DATA_HOME/ollie/tmp/)
@@ -90,7 +90,6 @@ Each 9P directory endpoint is backed by a named store implementing the `Store` i
 | `/m`  | `FlatDirStore`         | `Store`         |
 | `/p`  | `FlatDirStore`         | `Store`         |
 | `/sk` | `SkillStore`           | `Store`         |
-| `/t`  | `ToolStore`            | `Store`         |
 | `/tr` | `FlatDirStore`         | `Store`         |
 | `/tmp`| `FlatDirStore`         | `Store`         |
 | `/u`  | `UtilStore`            | `Store`         |
diff --git a/server.go b/server.go
index cd3f3d7..b737d50 100644
--- a/server.go
+++ b/server.go
@@ -327,6 +327,35 @@ func (s *Server) sessionFileStore(sessID string) (store.RunnableStore, bool) {
 	return st, true
 }
 
+// sessionAllowTools returns the allowTools set for a session, or nil if unrestricted.
+func (s *Server) sessionAllowTools(sessID string) map[string]bool {
+	sess := s.sessionStore.Session(sessID)
+	if sess == nil || len(sess.AllowTools) == 0 {
+		return nil
+	}
+	m := make(map[string]bool, len(sess.AllowTools))
+	for _, t := range sess.AllowTools {
+		m[t] = true
+	}
+	return m
+}
+
+// filterToolIndex filters a tool index (## name\n...\n\n sections) to only include allowed tools.
+func filterToolIndex(data []byte, allowed map[string]bool) []byte {
+	var out []byte
+	for _, section := range strings.Split(string(data), "## ") {
+		if section == "" {
+			continue
+		}
+		name, _, _ := strings.Cut(section, "\n")
+		if allowed[name] {
+			out = append(out, "## "...)
+			out = append(out, section...)
+		}
+	}
+	return out
+}
+
 // storeRead opens an entry in a store and reads it.
 func storeRead(s store.Store, name string) ([]byte, error) {
 	e, err := s.Open(name)
@@ -541,8 +570,6 @@ func (s *Server) pathType(path string) string {
 		return "dir"
 	case len(parts) == 1 && parts[0] == "sk":
 		return "dir"
-	case len(parts) == 1 && parts[0] == "t":
-		return "dir"
 	case len(parts) == 1 && parts[0] == "u":
 		return "dir"
 	case len(parts) == 2 && parts[0] == "u":
@@ -588,22 +615,22 @@ func (s *Server) pathType(path string) string {
 		if _, err := s.skillStore.Stat(parts[1]); err == nil {
 			return "file"
 		}
-	case len(parts) == 2 && parts[0] == "t":
-		if info, err := s.toolStore.Stat(parts[1]); err == nil {
-			if info.IsDir() {
-				return "dir"
-			}
-			return "file"
-		}
-	case len(parts) == 3 && parts[0] == "t":
-		if info, err := s.toolStore.Stat(parts[1] + "/" + parts[2]); err == nil {
-			if info.IsDir() {
-				return "dir"
-			}
-			return "file"
-		}
 	case len(parts) == 3 && parts[0] == "s":
-		if sfs, ok := s.sessionFileStore(parts[1]); ok {
+		if parts[2] == "t" {
+			// /s/{sid}/t is the tools directory
+			if s.sessionStore.Session(parts[1]) != nil {
+				return "dir"
+			}
+		} else if strings.HasPrefix(parts[2], "t/") {
+			// /s/{sid}/t/{rest} — tool file or subdir
+			rel := strings.TrimPrefix(parts[2], "t/")
+			if info, err := s.toolStore.Stat(rel); err == nil {
+				if info.IsDir() {
+					return "dir"
+				}
+				return "file"
+			}
+		} else if sfs, ok := s.sessionFileStore(parts[1]); ok {
 			if _, err := sfs.Stat(parts[2]); err == nil {
 				return "file"
 			}
@@ -731,23 +758,27 @@ func (s *Server) create(cs *connState, fc *plan9.Fcall) *plan9.Fcall {
 		return errFcall(fc, "bad fid")
 	}
 	if fc.Perm&plan9.DMDIR != 0 {
-		if f.path == "/t" || strings.HasPrefix(f.path, "/t/") {
-			rel := strings.TrimPrefix(f.path, "/t")
-			if rel == "" {
-				rel = fc.Name
-			} else {
-				rel = rel[1:] + "/" + fc.Name // strip leading /
+		// mkdir under session tool directory: /s/{sid}/t or /s/{sid}/t/...
+		if strings.HasPrefix(f.path, "/s/") {
+			parts := strings.SplitN(strings.TrimPrefix(f.path, "/s/"), "/", 3)
+			if (len(parts) == 2 && parts[1] == "t") || (len(parts) == 3 && parts[1] == "t") {
+				var rel string
+				if len(parts) == 2 {
+					rel = fc.Name
+				} else {
+					rel = parts[2] + "/" + fc.Name
+				}
+				dir := filepath.Join(s.toolStore.dir, rel)
+				if err := os.MkdirAll(dir, 0755); err != nil {
+					return errFcall(fc, err.Error())
+				}
+				newPath := pathJoin(f.path, fc.Name)
+				qid := plan9.Qid{Type: QTDir, Path: qidPath(newPath)}
+				f.path = newPath
+				f.qid = qid
+				f.mode = fc.Mode
+				return &plan9.Fcall{Type: plan9.Rcreate, Tag: fc.Tag, Qid: qid}
 			}
-			dir := filepath.Join(s.toolStore.dir, rel)
-			if err := os.MkdirAll(dir, 0755); err != nil {
-				return errFcall(fc, err.Error())
-			}
-			newPath := pathJoin(f.path, fc.Name)
-			qid := plan9.Qid{Type: QTDir, Path: qidPath(newPath)}
-			f.path = newPath
-			f.qid = qid
-			f.mode = fc.Mode
-			return &plan9.Fcall{Type: plan9.Rcreate, Tag: fc.Tag, Qid: qid}
 		}
 		return errFcall(fc, "mkdir not supported")
 	}
@@ -764,10 +795,6 @@ func (s *Server) create(cs *connState, fc *plan9.Fcall) *plan9.Fcall {
 		if err := s.memStore.Create(fc.Name); err != nil {
 			return errFcall(fc, err.Error())
 		}
-	case "/t":
-		if err := s.toolStore.Create(fc.Name); err != nil {
-			return errFcall(fc, err.Error())
-		}
 	case "/tmp":
 		if err := s.tmpStore.Create(fc.Name); err != nil {
 			return errFcall(fc, err.Error())
@@ -777,10 +804,19 @@ func (s *Server) create(cs *connState, fc *plan9.Fcall) *plan9.Fcall {
 			return errFcall(fc, err.Error())
 		}
 	default:
-		if strings.HasPrefix(f.path, "/t/") {
-			rel := strings.TrimPrefix(f.path, "/t/") + "/" + fc.Name
-			if err := s.toolStore.Create(rel); err != nil {
-				return errFcall(fc, err.Error())
+		// Tool creates under session: /s/{sid}/t or /s/{sid}/t/...
+		if strings.HasPrefix(f.path, "/s/") {
+			parts := strings.SplitN(strings.TrimPrefix(f.path, "/s/"), "/", 3)
+			if (len(parts) == 2 && parts[1] == "t") || (len(parts) == 3 && parts[1] == "t") {
+				var rel string
+				if len(parts) == 2 {
+					rel = fc.Name
+				} else {
+					rel = parts[2] + "/" + fc.Name
+				}
+				if err := s.toolStore.Create(rel); err != nil {
+					return errFcall(fc, err.Error())
+				}
 			}
 		}
 	}
@@ -880,16 +916,6 @@ func (s *Server) read(cs *connState, fc *plan9.Fcall, ctx context.Context) *plan
 		return s.readSlice(fc, content)
 	}
 
-	// Tool files are served from the tool store.
-	if strings.HasPrefix(path, "/t/") {
-		s.log.Debug("Tread path=%q offset=%d count=%d", path, fc.Offset, fc.Count)
-		content, err := storeReadCtx(ctx, s.toolStore, strings.TrimPrefix(path, "/t/"))
-		if err != nil {
-			return errFcall(fc, err.Error())
-		}
-		return s.readSlice(fc, content)
-	}
-
 	// Util files are served from the util store.
 	if strings.HasPrefix(path, "/u/") {
 		s.log.Debug("Tread path=%q offset=%d count=%d", path, fc.Offset, fc.Count)
@@ -934,6 +960,25 @@ func (s *Server) read(cs *connState, fc *plan9.Fcall, ctx context.Context) *plan
 	if strings.HasPrefix(path, "/s/") {
 		parts := strings.SplitN(strings.TrimPrefix(path, "/"), "/", 3)
 		if len(parts) == 3 {
+			// Tool files under session: /s/{id}/t/{tool}
+			if parts[2] == "t" || strings.HasPrefix(parts[2], "t/") {
+				rel := strings.TrimPrefix(parts[2], "t/")
+				if rel == "" {
+					// reading the directory itself as a file — shouldn't happen
+					return &plan9.Fcall{Type: plan9.Rread, Tag: fc.Tag, Count: 0}
+				}
+				s.log.Debug("Tread tool path=%q offset=%d count=%d", path, fc.Offset, fc.Count)
+				content, err := storeReadCtx(ctx, s.toolStore, rel)
+				if err != nil {
+					return errFcall(fc, err.Error())
+				}
+				if rel == "idx" {
+					if allowed := s.sessionAllowTools(parts[1]); allowed != nil {
+						content = filterToolIndex(content, allowed)
+					}
+				}
+				return s.readSlice(fc, content)
+			}
 			s.log.Debug("Tread session file path=%q offset=%d count=%d", path, fc.Offset, fc.Count)
 			sfs, ok := s.sessionFileStore(parts[1])
 			if !ok {
@@ -1093,26 +1138,25 @@ func (s *Server) wstat(cs *connState, fc *plan9.Fcall) *plan9.Fcall {
 		f.qid.Path = qidPath(f.path)
 		cs.mu.Unlock()
 
-	case strings.HasPrefix(f.path, "/t/"):
-		oldRel := strings.TrimPrefix(f.path, "/t/")
-		parentRel := oldRel[:len(oldRel)-len(oldName)]
-		newRel := parentRel + newDir.Name
-		if err := s.toolStore.Rename(oldRel, newRel); err != nil {
-			return errFcall(fc, err.Error())
-		}
-		cs.mu.Lock()
-		f.path = "/t/" + newRel
-		f.qid.Path = qidPath(f.path)
-		cs.mu.Unlock()
-
-	case strings.HasPrefix(f.path, "/s/") && f.path != "/s/new":
-		// Session directory rename: /s/{old} -> /s/{new}
-		parts := strings.SplitN(strings.TrimPrefix(f.path, "/"), "/", 3)
-		if len(parts) != 2 || parts[0] != "s" {
-			return errFcall(fc, "rename not supported")
-		}
-		if err := s.sessionStore.Rename(parts[1], newDir.Name); err != nil {
-			return errFcall(fc, err.Error())
+	case strings.HasPrefix(f.path, "/s/"):
+		parts := strings.SplitN(strings.TrimPrefix(f.path, "/s/"), "/", 3)
+		if len(parts) == 3 && parts[1] == "t" {
+			// Tool rename under session: /s/{sid}/t/{rel}
+			oldRel := parts[2]
+			parentRel := oldRel[:len(oldRel)-len(oldName)]
+			newRel := parentRel + newDir.Name
+			if err := s.toolStore.Rename(oldRel, newRel); err != nil {
+				return errFcall(fc, err.Error())
+			}
+			cs.mu.Lock()
+			f.path = "/s/" + parts[0] + "/t/" + newRel
+			f.qid.Path = qidPath(f.path)
+			cs.mu.Unlock()
+		} else if len(parts) == 1 && f.path != "/s/new" {
+			// Session directory rename: /s/{old} -> /s/{new}
+			if err := s.sessionStore.Rename(parts[0], newDir.Name); err != nil {
+				return errFcall(fc, err.Error())
+			}
 		}
 
 	default:
@@ -1187,18 +1231,28 @@ func (s *Server) remove(cs *connState, fc *plan9.Fcall) *plan9.Fcall {
 		err = s.memStore.Delete(pathBase(path))
 	case strings.HasPrefix(path, "/sk/"):
 		err = s.skillStore.Delete(pathBase(path))
-	case strings.HasPrefix(path, "/t/"):
-		err = s.toolStore.Delete(strings.TrimPrefix(path, "/t/"))
 	case strings.HasPrefix(path, "/tmp/"):
 		err = s.tmpStore.Delete(pathBase(path))
 	case strings.HasPrefix(path, "/tr/"):
 		err = s.transcriptStore.Delete(pathBase(path))
 	case strings.HasPrefix(path, "/s/") && path != "/s/new":
-		// If path is /s/{id}/{file}, it's a synthetic session file — no-op so
-		// that "rm -r s/{id}" can proceed to remove the directory itself, which
-		// triggers the actual session kill via Delete({id}).
-		parts := strings.SplitN(strings.TrimPrefix(path, "/s/"), "/", 2)
-		if len(parts) == 2 {
+		parts := strings.SplitN(strings.TrimPrefix(path, "/s/"), "/", 3)
+		if len(parts) >= 2 && (parts[1] == "t" || strings.HasPrefix(parts[1], "t/")) {
+			// Tool remove: /s/{sid}/t/{tool}
+			// Reconstruct: parts[0]=sid, rest starts with t/...
+			// Actually with SplitN(..., 3): parts = [sid, "t", rest] or [sid, "t"]
+			// But we split on /s/ prefix first, so path="/s/sid/t/file" -> "sid/t/file" split into ["sid","t","file"] or ["sid","t/file"]
+			// Wait — SplitN("sid/t/file", "/", 3) = ["sid", "t", "file"]
+			// SplitN("sid/t/sub/file", "/", 3) = ["sid", "t", "sub/file"]
+			if len(parts) == 2 && parts[1] == "t" {
+				err = nil // can't remove the t/ dir itself
+			} else if len(parts) == 3 && parts[1] == "t" {
+				err = s.toolStore.Delete(parts[2])
+			} else {
+				err = nil
+			}
+		} else if len(parts) >= 2 {
+			// Session file remove
 			err = nil // synthetic file; let rm -r continue
 		} else {
 			err = s.sessionStore.Delete(parts[0])
@@ -1240,11 +1294,6 @@ func (s *Server) handleWrite(path, input string) error {
 		return storeWrite(s.skillStore, pathBase(path), []byte(input))
 	}
 
-	// Tool file writes go to the tool store.
-	if strings.HasPrefix(path, "/t/") {
-		return storeWrite(s.toolStore, strings.TrimPrefix(path, "/t/"), []byte(input))
-	}
-
 	// Tmp file writes go to the tmp store.
 	if strings.HasPrefix(path, "/tmp/") {
 		return storeWrite(s.tmpStore, pathBase(path), []byte(input))
@@ -1254,6 +1303,11 @@ func (s *Server) handleWrite(path, input string) error {
 	if strings.HasPrefix(path, "/s/") {
 		parts := strings.SplitN(strings.TrimPrefix(path, "/"), "/", 3)
 		if len(parts) == 3 {
+			// Tool file writes: /s/{id}/t/{tool}
+			if strings.HasPrefix(parts[2], "t/") {
+				rel := strings.TrimPrefix(parts[2], "t/")
+				return storeWrite(s.toolStore, rel, []byte(input))
+			}
 			sfs, ok := s.sessionFileStore(parts[1])
 			if !ok {
 				return fmt.Errorf("session not found: %s", parts[1])
@@ -1295,7 +1349,6 @@ func (s *Server) readDir(path string, offset uint64, count uint32) []byte {
 		dirs = append(dirs, makeDir("p", "/p", true, plan9.DMDIR|0555))
 		dirs = append(dirs, makeDir("s", "/s", true, plan9.DMDIR|0555))
 		dirs = append(dirs, makeDir("sk", "/sk", true, plan9.DMDIR|0555))
-		dirs = append(dirs, makeDir("t", "/t", true, plan9.DMDIR|0777))
 		dirs = append(dirs, makeDir("tmp", "/tmp", true, plan9.DMDIR|0755))
 		dirs = append(dirs, makeDir("u", "/u", true, plan9.DMDIR|0755))
 		dirs = append(dirs, makeDir("x", "/x", true, plan9.DMDIR|0555))
@@ -1335,21 +1388,6 @@ func (s *Server) readDir(path string, offset uint64, count uint32) []byte {
 			}
 			dirs = append(dirs, makeDir(e.Name(), "/sk/"+e.Name(), false, mode))
 		}
-	} else if path == "/t" {
-		entries, _ := s.toolStore.List()
-		for _, e := range entries {
-			mode := plan9.Perm(0777)
-			if e.Name() == "idx" {
-				mode = 0444
-			}
-			dirs = append(dirs, makeDir(e.Name(), "/t/"+e.Name(), e.IsDir(), mode|plan9.Perm(boolToDir(e.IsDir()))))
-		}
-	} else if strings.HasPrefix(path, "/t/") {
-		rel := strings.TrimPrefix(path, "/t/")
-		entries, _ := s.toolStore.ListDir(rel)
-		for _, e := range entries {
-			dirs = append(dirs, makeDir(e.Name(), path+"/"+e.Name(), e.IsDir(), 0777|plan9.Perm(boolToDir(e.IsDir()))))
-		}
 	} else if path == "/tmp" {
 		entries, _ := s.tmpStore.List()
 		for _, e := range entries {
@@ -1395,15 +1433,46 @@ func (s *Server) readDir(path string, offset uint64, count uint32) []byte {
 			}
 			dirs = append(dirs, makeDir(e.Name(), "/s/"+e.Name(), e.IsDir(), perm))
 		}
-	} else {
-		// Session subdirectory: /s/{sessid}
-		sessID := pathBase(path)
-		if sfs, ok := s.sessionFileStore(sessID); ok {
-			entries, _ := sfs.List()
-			for _, e := range entries {
-				info, _ := e.Info()
-				dirs = append(dirs, makeDir(e.Name(), path+"/"+e.Name(), false, plan9.Perm(info.Mode())))
+	} else if strings.HasPrefix(path, "/s/") {
+		// /s/{sid}/t — list tools
+		// /s/{sid}/t/{subdir} — list tool subdirectory
+		// /s/{sid} — list session files + t/
+		parts := strings.SplitN(strings.TrimPrefix(path, "/s/"), "/", 3)
+		if len(parts) >= 2 && parts[1] == "t" {
+			if len(parts) == 2 {
+				// /s/{sid}/t
+				entries, _ := s.toolStore.List()
+				allowed := s.sessionAllowTools(parts[0])
+				for _, e := range entries {
+					if e.Name() == "idx" {
+						dirs = append(dirs, makeDir(e.Name(), path+"/"+e.Name(), false, 0444))
+						continue
+					}
+					if allowed != nil && !allowed[e.Name()] {
+						continue
+					}
+					mode := plan9.Perm(0777)
+					dirs = append(dirs, makeDir(e.Name(), path+"/"+e.Name(), e.IsDir(), mode|plan9.Perm(boolToDir(e.IsDir()))))
+				}
+			} else {
+				// /s/{sid}/t/{subdir...}
+				rel := parts[2]
+				entries, _ := s.toolStore.ListDir(rel)
+				for _, e := range entries {
+					dirs = append(dirs, makeDir(e.Name(), path+"/"+e.Name(), e.IsDir(), 0777|plan9.Perm(boolToDir(e.IsDir()))))
+				}
 			}
+		} else if len(parts) == 1 {
+			// /s/{sid} — session files + t/
+			sessID := parts[0]
+			if sfs, ok := s.sessionFileStore(sessID); ok {
+				entries, _ := sfs.List()
+				for _, e := range entries {
+					info, _ := e.Info()
+					dirs = append(dirs, makeDir(e.Name(), path+"/"+e.Name(), false, plan9.Perm(info.Mode())))
+				}
+			}
+			dirs = append(dirs, makeDir("t", path+"/t", true, plan9.DMDIR|0777))
 		}
 	}
 
@@ -1454,8 +1523,13 @@ func (s *Server) makeStat(path string) plan9.Dir {
 	var mode plan9.Perm
 	if isDir {
 		qid.Type = QTDir
-		if path == "/t" || strings.HasPrefix(path, "/t/") {
-			mode = plan9.DMDIR | 0777
+		if strings.HasPrefix(path, "/s/") {
+			parts := strings.SplitN(strings.TrimPrefix(path, "/s/"), "/", 3)
+			if (len(parts) == 2 && parts[1] == "t") || (len(parts) == 3 && parts[1] == "t") {
+				mode = plan9.DMDIR | 0777
+			} else {
+				mode = plan9.DMDIR | 0555
+			}
 		} else if path == "/a" || path == "/m" || path == "/tmp" || path == "/u" {
 			mode = plan9.DMDIR | 0755
 		} else {
@@ -1487,10 +1561,15 @@ func (s *Server) makeStat(path string) plan9.Dir {
 				mode = 0444
 			} else if strings.HasPrefix(path, "/sk/") {
 				mode = 0666
-			} else if path == "/t/idx" {
-				mode = 0444
-			} else if strings.HasPrefix(path, "/t/") {
-				mode = 0777
+			} else if strings.HasPrefix(path, "/s/") {
+				parts := strings.SplitN(strings.TrimPrefix(path, "/s/"), "/", 3)
+				if len(parts) == 3 && parts[1] == "t" && parts[2] == "idx" {
+					mode = 0444
+				} else if len(parts) == 3 && parts[1] == "t" {
+					mode = 0777
+				} else {
+					mode = 0444
+				}
 			} else if strings.HasPrefix(path, "/u/") {
 				mode = 0555
 			} else if strings.HasPrefix(path, "/x/") {
@@ -1561,9 +1640,12 @@ func (s *Server) makeStat(path string) plan9.Dir {
 			if content, err := storeRead(s.skillStore, base); err == nil {
 				dir.Length = uint64(len(content))
 			}
-		case strings.HasPrefix(path, "/t/"):
-			if content, err := storeRead(s.toolStore, strings.TrimPrefix(path, "/t/")); err == nil {
-				dir.Length = uint64(len(content))
+		case strings.HasPrefix(path, "/s/") && strings.Contains(path, "/t/"):
+			parts := strings.SplitN(strings.TrimPrefix(path, "/s/"), "/", 3)
+			if len(parts) == 3 && parts[1] == "t" {
+				if content, err := storeRead(s.toolStore, parts[2]); err == nil {
+					dir.Length = uint64(len(content))
+				}
 			}
 		case strings.HasPrefix(path, "/u/"):
 			if content, err := storeRead(s.utilStore, base); err == nil {
diff --git a/store/session.go b/store/session.go
index 852ff20..e114557 100644
--- a/store/session.go
+++ b/store/session.go
@@ -29,6 +29,7 @@ type Session struct {
 	ChatOffset int
 	plan       []byte
 	prevPrompt []byte // last submitted prompt; overwritten on each new submission
+	AllowTools []string // if non-empty, only these tools are visible/executable
 }
 
 func NewSession(id string, core agent.Core, ctx context.Context, cancel context.CancelFunc) *Session {
@@ -356,6 +357,7 @@ func (s *SessionStore) createSession(args []string) error {
 	}
 
 	var core agent.Core
+	var allowTools []string
 	if s.cfg.NewCore != nil {
 		var err error
 		core, err = s.cfg.NewCore(sessID, agentName, cwd)
@@ -380,6 +382,9 @@ func (s *SessionStore) createSession(args []string) error {
 		}
 
 		cfg := LoadAgentConfig(s.cfg.AgentsDir, agentName, nil)
+		if cfg != nil {
+			allowTools = cfg.AllowTools
+		}
 
 		var execOpts []execute.Option
 		if s.cfg.Strict {
@@ -388,6 +393,12 @@ func (s *SessionStore) createSession(args []string) error {
 		if s.cfg.Yolo {
 			execOpts = append(execOpts, execute.WithYolo())
 		}
+		if cfg != nil && len(cfg.AllowExecutors) > 0 {
+			execOpts = append(execOpts, execute.WithAllowExecutors(cfg.AllowExecutors))
+		}
+		if cfg != nil && len(cfg.AllowTools) > 0 {
+			execOpts = append(execOpts, execute.WithAllowTools(cfg.AllowTools))
+		}
 		newDisp := tools.NewDispatcherFunc(map[string]func() tools.Server{
 			"execute": execute.Decl(cwd, execOpts...),
 		})
@@ -409,6 +420,7 @@ func (s *SessionStore) createSession(args []string) error {
 
 	ctx, cancel := context.WithCancel(context.Background())
 	sess := NewSession(sessID, core, ctx, cancel)
+	sess.AllowTools = allowTools
 
 	s.mu.Lock()
 	s.sessions[sessID] = sess