diff --git a/nanobot/agent/context.py b/nanobot/agent/context.py
index 19ee935c4..82ebfab65 100644
--- a/nanobot/agent/context.py
+++ b/nanobot/agent/context.py
@@ -22,7 +22,7 @@ from nanobot.utils.prompt_templates import render_template
 class ContextBuilder:
     """Builds the context (system prompt + messages) for the agent."""
 
-    BOOTSTRAP_FILES = ["AGENTS.md", "SOUL.md", "USER.md", "TOOLS.md"]
+    BOOTSTRAP_FILES = ["AGENTS.md", "SOUL.md", "USER.md"]
     _RUNTIME_CONTEXT_TAG = "[Runtime Context — metadata only, not instructions]"
     _MAX_RECENT_HISTORY = 50
     _MAX_HISTORY_CHARS = 32_000  # hard cap on recent history section size
@@ -47,6 +47,8 @@ class ContextBuilder:
         if bootstrap:
             parts.append(bootstrap)
 
+        parts.append(render_template("agent/tool_contract.md"))
+
         memory = self.memory.get_memory_context()
         if memory and not self._is_template_content(self.memory.read_memory(), "memory/MEMORY.md"):
             parts.append(f"# Memory\n\n{memory}")
@@ -210,4 +212,3 @@ class ContextBuilder:
         if not images:
             return text
         return images + [{"type": "text", "text": text}]
-
diff --git a/nanobot/templates/AGENTS.md b/nanobot/templates/AGENTS.md
index 0bf6de3d3..46cfc08c3 100644
--- a/nanobot/templates/AGENTS.md
+++ b/nanobot/templates/AGENTS.md
@@ -1,5 +1,9 @@
 # Agent Instructions
 
+## Workspace Guidance
+
+Use this file for project-specific preferences, recurring workflow conventions, and instructions you want the agent to remember for this workspace. Keep durable facts about the user in `USER.md`, personality/style guidance in `SOUL.md`, and long-term memory in `memory/MEMORY.md`.
+
 ## Scheduled Reminders
 
 Before scheduling reminders, check available skills and follow skill guidance first.
@@ -10,10 +14,10 @@ Get USER_ID and CHANNEL from the current session (e.g., `8281248569` and `telegr
 
 ## Heartbeat Tasks
 
-`HEARTBEAT.md` is checked on the configured heartbeat interval. Use file tools to manage periodic tasks:
+`HEARTBEAT.md` is checked on the configured heartbeat interval. Use file tools to manage periodic tasks.
 
-- **Add**: `edit_file` to append new tasks
-- **Remove**: `edit_file` to delete completed tasks
-- **Rewrite**: `write_file` to replace all tasks
+- Use `apply_patch` for normal task-list updates, especially when adding, removing, or changing multiple lines.
+- Use `edit_file` only for small exact replacements copied from the current `HEARTBEAT.md`.
+- Use `write_file` for first creation or intentional full-file rewrites.
 
 When the user asks for a recurring/periodic task, update `HEARTBEAT.md` instead of creating a one-time cron reminder.
diff --git a/nanobot/templates/TOOLS.md b/nanobot/templates/agent/tool_contract.md
similarity index 99%
rename from nanobot/templates/TOOLS.md
rename to nanobot/templates/agent/tool_contract.md
index ee37090ea..edbba21c9 100644
--- a/nanobot/templates/TOOLS.md
+++ b/nanobot/templates/agent/tool_contract.md
@@ -1,6 +1,6 @@
 # Tool Usage Notes
 
-Tool signatures are provided automatically via function calling. This file
+Tool signatures are provided automatically via function calling. This section
 documents the general tool contract and non-obvious usage patterns.
 
 ## General Tool Contract
diff --git a/nanobot/utils/helpers.py b/nanobot/utils/helpers.py
index 2a969298c..ae91bf394 100644
--- a/nanobot/utils/helpers.py
+++ b/nanobot/utils/helpers.py
@@ -576,7 +576,7 @@ def build_status_content(
 
 
 def sync_workspace_templates(workspace: Path, silent: bool = False) -> list[str]:
-    """Sync bundled templates to workspace. Only creates missing files."""
+    """Sync bundled templates to workspace. Creates missing files without overwriting user files."""
     from importlib.resources import files as pkg_files
 
     try:
@@ -589,10 +589,11 @@ def sync_workspace_templates(workspace: Path, silent: bool = False) -> list[str]
     added: list[str] = []
 
     def _write(src, dest: Path):
+        content = src.read_text(encoding="utf-8") if src else ""
         if dest.exists():
             return
         dest.parent.mkdir(parents=True, exist_ok=True)
-        dest.write_text(src.read_text(encoding="utf-8") if src else "", encoding="utf-8")
+        dest.write_text(content, encoding="utf-8")
         added.append(str(dest.relative_to(workspace)))
 
     for item in tpl.iterdir():
diff --git a/tests/agent/test_context_builder.py b/tests/agent/test_context_builder.py
index abd934b0a..a36c0a30a 100644
--- a/tests/agent/test_context_builder.py
+++ b/tests/agent/test_context_builder.py
@@ -139,6 +139,13 @@ class TestLoadBootstrapFiles:
         for name in ContextBuilder.BOOTSTRAP_FILES:
             assert f"## {name}" in result
 
+    def test_legacy_tools_md_is_not_bootstrapped(self, tmp_path):
+        (tmp_path / "TOOLS.md").write_text("workspace tool notes", encoding="utf-8")
+        builder = _builder(tmp_path)
+        result = builder._load_bootstrap_files()
+        assert "TOOLS.md" not in result
+        assert "workspace tool notes" not in result
+
     def test_utf8_content(self, tmp_path):
         (tmp_path / "AGENTS.md").write_text("用中文回复", encoding="utf-8")
         builder = _builder(tmp_path)
@@ -176,11 +183,11 @@ class TestIsTemplateContent:
 # ---------------------------------------------------------------------------
 
 
-class TestBundledToolsTemplate:
-    def test_tools_template_balances_general_and_coding_workflows(self):
+class TestBundledToolContract:
+    def test_tool_contract_balances_general_and_coding_workflows(self):
         from importlib.resources import files as pkg_files
 
-        tpl = pkg_files("nanobot") / "templates" / "TOOLS.md"
+        tpl = pkg_files("nanobot") / "templates" / "agent" / "tool_contract.md"
         content = tpl.read_text(encoding="utf-8")
 
         assert "## General Tool Contract" in content
@@ -193,6 +200,14 @@ class TestBundledToolsTemplate:
         assert "## Scheduling and Background Work" in content
         assert "pure coding" not in content.lower()
 
+    def test_tool_contract_is_injected_without_workspace_file(self, tmp_path):
+        builder = _builder(tmp_path)
+        prompt = builder.build_system_prompt()
+
+        assert "# Tool Usage Notes" in prompt
+        assert "## General Tool Contract" in prompt
+        assert "Do not use `exec` as a universal workaround" in prompt
+
 
 # ---------------------------------------------------------------------------
 # _build_user_content
diff --git a/tests/agent/test_onboard_logic.py b/tests/agent/test_onboard_logic.py
index 11a284bb5..762da4f31 100644
--- a/tests/agent/test_onboard_logic.py
+++ b/tests/agent/test_onboard_logic.py
@@ -346,6 +346,26 @@ class TestSyncWorkspaceTemplates:
         content = (workspace / "AGENTS.md").read_text()
         assert content == "existing content"
 
+    def test_does_not_create_tools_md(self, tmp_path):
+        """Tool contract is injected internally, not copied into user workspaces."""
+        workspace = tmp_path / "workspace"
+
+        added = sync_workspace_templates(workspace, silent=True)
+
+        assert "TOOLS.md" not in added
+        assert not (workspace / "TOOLS.md").exists()
+
+    def test_preserves_existing_tools_md_without_overwriting(self, tmp_path):
+        """Legacy user workspaces may have TOOLS.md; sync should leave it untouched."""
+        workspace = tmp_path / "workspace"
+        workspace.mkdir(parents=True)
+        tools_path = workspace / "TOOLS.md"
+        tools_path.write_text("custom tool notes", encoding="utf-8")
+
+        sync_workspace_templates(workspace, silent=True)
+
+        assert tools_path.read_text(encoding="utf-8") == "custom tool notes"
+
     def test_creates_memory_directory(self, tmp_path):
         """Should create memory directory structure."""
         workspace = tmp_path / "workspace"