diff --git a/scripts/bash/update-agent-context.sh b/scripts/bash/update-agent-context.sh
index da06ed4697..b0ef4b422a 100644
--- a/scripts/bash/update-agent-context.sh
+++ b/scripts/bash/update-agent-context.sh
@@ -84,7 +84,7 @@ AGY_FILE="$REPO_ROOT/.agent/rules/specify-rules.md"
 BOB_FILE="$AGENTS_FILE"
 VIBE_FILE="$REPO_ROOT/.vibe/agents/specify-agents.md"
 KIMI_FILE="$REPO_ROOT/KIMI.md"
-TRAE_FILE="$REPO_ROOT/.trae/rules/AGENTS.md"
+TRAE_FILE="$REPO_ROOT/.trae/rules/project_rules.md"
 IFLOW_FILE="$REPO_ROOT/IFLOW.md"
 FORGE_FILE="$AGENTS_FILE"
 
diff --git a/scripts/powershell/update-agent-context.ps1 b/scripts/powershell/update-agent-context.ps1
index 342ee5464d..12caa306da 100644
--- a/scripts/powershell/update-agent-context.ps1
+++ b/scripts/powershell/update-agent-context.ps1
@@ -65,7 +65,7 @@ $AGY_FILE      = Join-Path $REPO_ROOT '.agent/rules/specify-rules.md'
 $BOB_FILE      = Join-Path $REPO_ROOT 'AGENTS.md'
 $VIBE_FILE     = Join-Path $REPO_ROOT '.vibe/agents/specify-agents.md'
 $KIMI_FILE     = Join-Path $REPO_ROOT 'KIMI.md'
-$TRAE_FILE     = Join-Path $REPO_ROOT '.trae/rules/AGENTS.md'
+$TRAE_FILE     = Join-Path $REPO_ROOT '.trae/rules/project_rules.md'
 $IFLOW_FILE    = Join-Path $REPO_ROOT 'IFLOW.md'
 $FORGE_FILE    = Join-Path $REPO_ROOT 'AGENTS.md'
 
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 1c62a4a3be..a3aa7d94f9 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1287,7 +1287,7 @@ def init(
         step_num = 2
 
     # Determine skill display mode for the next-steps panel.
-    # Skills integrations (codex, kimi, agy) should show skill invocation syntax.
+    # Skills integrations (codex, kimi, agy, trae) should show skill invocation syntax.
     from .integrations.base import SkillsIntegration as _SkillsInt
     _is_skills_integration = isinstance(resolved_integration, _SkillsInt)
 
@@ -1295,7 +1295,8 @@ def init(
     claude_skill_mode = selected_ai == "claude" and (ai_skills or _is_skills_integration)
     kimi_skill_mode = selected_ai == "kimi"
     agy_skill_mode = selected_ai == "agy" and _is_skills_integration
-    native_skill_mode = codex_skill_mode or claude_skill_mode or kimi_skill_mode or agy_skill_mode
+    trae_skill_mode = selected_ai == "trae"
+    native_skill_mode = codex_skill_mode or claude_skill_mode or kimi_skill_mode or agy_skill_mode or trae_skill_mode
 
     if codex_skill_mode and not ai_skills:
         # Integration path installed skills; show the helpful notice
@@ -1307,7 +1308,7 @@ def init(
     usage_label = "skills" if native_skill_mode else "slash commands"
 
     def _display_cmd(name: str) -> str:
-        if codex_skill_mode or agy_skill_mode:
+        if codex_skill_mode or agy_skill_mode or trae_skill_mode:
             return f"$speckit-{name}"
         if claude_skill_mode:
             return f"/speckit-{name}"
diff --git a/src/specify_cli/integrations/trae/__init__.py b/src/specify_cli/integrations/trae/__init__.py
index 7037eecb8c..343a7527f8 100644
--- a/src/specify_cli/integrations/trae/__init__.py
+++ b/src/specify_cli/integrations/trae/__init__.py
@@ -1,21 +1,40 @@
-"""Trae IDE integration."""
+"""Trae IDE integration. — skills-based agent.
 
-from ..base import MarkdownIntegration
+Trae IDE uses ``.trae/skills/speckit-<name>/SKILL.md`` layout.
+In the Specify CLI Trae integration, explicit command support was deprecated
+since v0.5.1; ``--skills`` defaults to ``True``.
+"""
 
+from __future__ import annotations
+from ..base import IntegrationOption, SkillsIntegration
+
+
+class TraeIntegration(SkillsIntegration):
+    """Integration for Trae IDE."""
 
-class TraeIntegration(MarkdownIntegration):
     key = "trae"
     config = {
         "name": "Trae",
         "folder": ".trae/",
-        "commands_subdir": "rules",
+        "commands_subdir": "skills",
         "install_url": None,
         "requires_cli": False,
     }
     registrar_config = {
-        "dir": ".trae/rules",
+        "dir": ".trae/skills",
         "format": "markdown",
         "args": "$ARGUMENTS",
-        "extension": ".md",
+        "extension": "/SKILL.md",
     }
-    context_file = ".trae/rules/AGENTS.md"
+    context_file = ".trae/rules/project_rules.md"
+
+    @classmethod
+    def options(cls) -> list[IntegrationOption]:
+        return [
+            IntegrationOption(
+                "--skills",
+                is_flag=True,
+                default=True,
+                help="Install as agent skills (default for trae since v0.5.1)",
+            ),
+        ]
diff --git a/src/specify_cli/integrations/trae/scripts/update-context.ps1 b/src/specify_cli/integrations/trae/scripts/update-context.ps1
index f72d96318e..ae9a3d1cd0 100644
--- a/src/specify_cli/integrations/trae/scripts/update-context.ps1
+++ b/src/specify_cli/integrations/trae/scripts/update-context.ps1
@@ -1,4 +1,4 @@
-# update-context.ps1 — Trae integration: create/update .trae/rules/AGENTS.md
+# update-context.ps1 — Trae integration: create/update .trae/rules/project_rules.md
 #
 # Thin wrapper that delegates to the shared update-agent-context script.
 # Activated in Stage 7 when the shared script uses integration.json dispatch.
diff --git a/src/specify_cli/integrations/trae/scripts/update-context.sh b/src/specify_cli/integrations/trae/scripts/update-context.sh
index b868a7c983..32e5c16b29 100755
--- a/src/specify_cli/integrations/trae/scripts/update-context.sh
+++ b/src/specify_cli/integrations/trae/scripts/update-context.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# update-context.sh — Trae integration: create/update .trae/rules/AGENTS.md
+# update-context.sh — Trae integration: create/update .trae/rules/project_rules.md
 #
 # Thin wrapper that delegates to the shared update-agent-context script.
 # Activated in Stage 7 when the shared script uses integration.json dispatch.
diff --git a/src/specify_cli/presets.py b/src/specify_cli/presets.py
index 0c8bba1757..137d1d22a8 100644
--- a/src/specify_cli/presets.py
+++ b/src/specify_cli/presets.py
@@ -717,7 +717,7 @@ def _register_skills(
         ai_skills_enabled = bool(init_opts.get("ai_skills"))
         registrar = CommandRegistrar()
         agent_config = registrar.AGENT_CONFIGS.get(selected_ai, {})
-        # Native skill agents (e.g. codex/kimi/agy) materialize brand-new
+        # Native skill agents (e.g. codex/kimi/agy/trae) materialize brand-new
         # preset skills in _register_commands() because their detected agent
         # directory is already the skills directory. This flag is only for
         # command-backed agents that also mirror commands into skills.
diff --git a/tests/integrations/test_integration_trae.py b/tests/integrations/test_integration_trae.py
index 307c3481db..74b8b41c3f 100644
--- a/tests/integrations/test_integration_trae.py
+++ b/tests/integrations/test_integration_trae.py
@@ -1,11 +1,11 @@
 """Tests for TraeIntegration."""
 
-from .test_integration_base_markdown import MarkdownIntegrationTests
+from .test_integration_base_skills import SkillsIntegrationTests
 
 
-class TestTraeIntegration(MarkdownIntegrationTests):
+class TestTraeIntegration(SkillsIntegrationTests):
     KEY = "trae"
     FOLDER = ".trae/"
-    COMMANDS_SUBDIR = "rules"
-    REGISTRAR_DIR = ".trae/rules"
-    CONTEXT_FILE = ".trae/rules/AGENTS.md"
+    COMMANDS_SUBDIR = "skills"
+    REGISTRAR_DIR = ".trae/skills"
+    CONTEXT_FILE = ".trae/rules/project_rules.md"
diff --git a/tests/test_agent_config_consistency.py b/tests/test_agent_config_consistency.py
index 8e293baa17..35d8c02f7e 100644
--- a/tests/test_agent_config_consistency.py
+++ b/tests/test_agent_config_consistency.py
@@ -139,7 +139,7 @@ def test_trae_in_agent_config(self):
         """AGENT_CONFIG should include trae with correct folder and commands_subdir."""
         assert "trae" in AGENT_CONFIG
         assert AGENT_CONFIG["trae"]["folder"] == ".trae/"
-        assert AGENT_CONFIG["trae"]["commands_subdir"] == "rules"
+        assert AGENT_CONFIG["trae"]["commands_subdir"] == "skills"
         assert AGENT_CONFIG["trae"]["requires_cli"] is False
         assert AGENT_CONFIG["trae"]["install_url"] is None
 
@@ -151,7 +151,7 @@ def test_trae_in_extension_registrar(self):
         trae_cfg = cfg["trae"]
         assert trae_cfg["format"] == "markdown"
         assert trae_cfg["args"] == "$ARGUMENTS"
-        assert trae_cfg["extension"] == ".md"
+        assert trae_cfg["extension"] == "/SKILL.md"
 
     def test_trae_in_agent_context_scripts(self):
         """Agent context scripts should support trae agent type."""