feat: enhance tool normalization and injection handling

- Introduced `_server_keys_for_enrichment` to extract and normalize server keys from tools, improving the enrichment process.
- Updated `_normalize_tools_list` to utilize the new enrichment function, ensuring tools are enriched with relevant identities based on server keys.
- Added `apply_inject_via_overlay` function to streamline the configuration of injection modes for agents, enhancing flexibility in tool setup.
- Adjusted tests to reflect changes in tool normalization and injection handling, ensuring consistent behavior across the codebase.
- This update aims to improve the robustness and clarity of tool management and injection processes.

Author: qdrddr

src/cyt/cyt_mcp/catalog.py

@@ -215,15 +215,37 @@ def _normalize_tool(tool: dict[str, Any]) -> dict[str, Any] | None:
     return normalized
 
 
+def _server_keys_for_enrichment(tools: Sequence[Any]) -> list[str]:
+    keys: set[str] = set()
+    for item in tools:
+        if not isinstance(item, dict):
+            continue
+        server_key = item.get("server_key")
+        if isinstance(server_key, str) and server_key.strip():
+            keys.add(server_key.strip())
+    try:
+        from cyt_mcp.config import load_known_mcp_server_keys
+
+        keys.update(load_known_mcp_server_keys())
+    except Exception:
+        pass
+    return sorted(keys, key=len, reverse=True)
+
+
 def _normalize_tools_list(tools: Sequence[Any]) -> list[dict[str, Any]]:
+    from cyt_mcp.tool_identity import enrich_tool_identity
+
     normalized: list[dict[str, Any]] = []
     for item in tools:
         if not isinstance(item, dict):
             continue
         tool = _normalize_tool(item)
         if tool is not None:
             normalized.append(tool)
-    return normalized
+    if not normalized:
+        return []
+    server_keys = _server_keys_for_enrichment(normalized)
+    return [enrich_tool_identity(tool, server_keys) for tool in normalized]
 
 
 def _filter_tools_by_permissions(

src/cyt/skills/catalog.py

@@ -629,6 +629,7 @@ def _build_registry_from_inline_sources(
     inline_sources: list[dict[str, str]],
     *,
     original_by_hash: dict[str, Path],
+    allow_ephemeral_paths: bool = False,
 ) -> list[SkillEntryRef]:
     """Build a skills registry from inline ``{path, content, content_sha256}`` sources."""
     if not inline_sources:
@@ -657,7 +658,7 @@ def _build_registry_from_inline_sources(
             continue
         from cyt.tiers.adapters.skills import is_ephemeral_skill_path
 
-        if is_ephemeral_skill_path(str(original_path)):
+        if not allow_ephemeral_paths and is_ephemeral_skill_path(str(original_path)):
             continue
         entry = _entry_from_rust_ref(
             ref,
@@ -699,10 +700,6 @@ def _build_registry_from_client_skills(
 
     for skill in client_skills:
         original_path = Path(skill["path"]).expanduser()
-        from cyt.tiers.adapters.skills import is_ephemeral_skill_path
-
-        if is_ephemeral_skill_path(str(original_path)):
-            continue
         content = skill["content"]
         content_hash = hashlib.sha256(content.encode("utf-8")).hexdigest()
         if content_hash in seen_content:
@@ -722,6 +719,7 @@ def _build_registry_from_client_skills(
         cfg,
         inline_sources,
         original_by_hash=original_by_hash,
+        allow_ephemeral_paths=True,
     )
 
 

src/cyt/testing/inject_via_maps.py

@@ -2,9 +2,18 @@
 
 from __future__ import annotations
 
+from typing import Any
+
 from cyt.config import inject_via_agents
 
 _agents = inject_via_agents()
 INJECT_VIA_ALL_HOOK: dict[str, str] = dict.fromkeys(_agents, "hook")
 INJECT_VIA_DEFAULT: dict[str, str] = dict(_agents)
 INJECT_VIA_ALL_PROXY: dict[str, str] = dict.fromkeys(_agents, "proxy")
+
+
+def apply_inject_via_overlay(config: dict[str, Any], inject_via: dict[str, str]) -> None:
+    """Write per-agent ``agents.<agent>.tools.inject_via`` (canonical config path)."""
+    agents = config.setdefault("agents", {})
+    for agent, mode in inject_via.items():
+        agents.setdefault(agent, {}).setdefault("tools", {})["inject_via"] = mode

src/tests/conftest.py

@@ -279,6 +279,7 @@ def isolated_maintenance_marker_path(config: dict) -> Path:
 def _isolate_hook_catalog_state(monkeypatch: pytest.MonkeyPatch) -> Iterator[None]:
     """Stop background catalog schedulers and clear in-memory hook caches."""
     from cyt.cloudflare.catalog import clear_cloudflare_catalog_cache
+    from cyt.cyt_mcp.catalog import clear_cyt_mcp_catalog_cache
     from cyt.executor.http import clear_executor_catalog_cache
     from cyt.mcpc.catalog import clear_mcpc_catalog_cache
     from cyt.tools.catalog_cache import clear_decomposed_catalog_cache
@@ -311,6 +312,7 @@ def _isolate_hook_catalog_state(monkeypatch: pytest.MonkeyPatch) -> Iterator[Non
 
     def _clear_all_hook_catalog_state() -> None:
         clear_cloudflare_catalog_cache()
+        clear_cyt_mcp_catalog_cache()
         clear_executor_catalog_cache()
         clear_mcpc_catalog_cache()
         clear_master_catalog_cache()

src/tests/unit/test_master_catalog.py

@@ -69,7 +69,6 @@ def test_build_master_tools_stamps_token_count() -> None:
 
 def test_get_master_tool_catalog_concatenates_configured_sources() -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "hook", "codex": "hook"}
     config["tools"]["enabled"] = True
     config["tools"]["hook"]["tools_from"] = ["mcpc", "executor"]
 
@@ -91,7 +90,6 @@ def test_get_master_tool_catalog_concatenates_configured_sources() -> None:
 
 def test_get_master_tool_catalog_returns_empty_list_not_none_on_cold_start() -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "hook", "codex": "hook"}
     config["tools"]["enabled"] = True
     config["tools"]["hook"]["tools_from"] = ["mcpc"]
 
@@ -103,7 +101,6 @@ def test_get_master_tool_catalog_returns_empty_list_not_none_on_cold_start() ->
 
 def test_rebuild_master_catalog_preserves_prior_source_on_empty_non_blocking_read() -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "hook", "codex": "hook"}
     config["tools"]["enabled"] = True
     config["tools"]["hook"]["tools_from"] = ["mcpc", "executor"]
 
@@ -136,7 +133,6 @@ def test_rebuild_master_catalog_preserves_prior_source_on_empty_non_blocking_rea
 
 def test_rebuild_master_catalog_drops_source_when_fingerprint_changes_and_read_empty() -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "hook", "codex": "hook"}
     config["tools"]["enabled"] = True
     config["tools"]["hook"]["tools_from"] = ["mcpc", "executor"]
 
@@ -172,7 +168,6 @@ def test_rebuild_master_catalog_drops_source_when_fingerprint_changes_and_read_e
 
 def test_rebuild_master_catalog_clears_stale_tools_when_all_sources_genuinely_empty() -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "hook", "codex": "hook"}
     config["tools"]["enabled"] = True
     config["tools"]["hook"]["tools_from"] = ["executor"]
 
@@ -201,7 +196,6 @@ def test_rebuild_master_catalog_clears_stale_tools_when_all_sources_genuinely_em
 
 def test_blocking_get_master_waits_for_in_progress_rebuild() -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "hook", "codex": "hook"}
     config["tools"]["enabled"] = True
     config["tools"]["hook"]["tools_from"] = ["mcpc"]
 

src/tests/unit/test_tools_hook_setup.py

@@ -7,6 +7,7 @@
 import pytest
 
 from cyt.config import load_config
+from cyt.testing.inject_via_maps import apply_inject_via_overlay
 from cyt.tools import hook_setup
 from cyt.tools.hook_setup import prompt_tools_hook_config
 
@@ -15,7 +16,10 @@ def test_prompt_tools_hook_config_preserves_multi_source_list_when_not_hook_mode
     monkeypatch: pytest.MonkeyPatch,
 ) -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "proxy", "codex": "proxy"}
+    apply_inject_via_overlay(
+        config,
+        {"cursor": "hook", "claude": "proxy", "codex": "proxy"},
+    )
     config["tools"]["hook"]["tools_from"] = ["mcpc", "executor"]
 
     overlay = prompt_tools_hook_config(config, context="setup", inject_mode="proxy")
@@ -27,7 +31,10 @@ def test_prompt_tools_hook_config_preserves_single_source_as_list_when_not_hook_
     monkeypatch: pytest.MonkeyPatch,
 ) -> None:
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "proxy", "codex": "proxy"}
+    apply_inject_via_overlay(
+        config,
+        {"cursor": "hook", "claude": "proxy", "codex": "proxy"},
+    )
     config["tools"]["hook"]["tools_from"] = ["mcpc"]
 
     overlay = prompt_tools_hook_config(config, context="setup", inject_mode="proxy")
@@ -78,7 +85,10 @@ def test_ensure_tools_hook_file_interactive_prompts_for_missing_cloudflare_url(
 
     config_path = tmp_path / "config.yaml"
     config = load_config()
-    config["pruning"]["inject_via"] = {"cursor": "hook", "claude": "hook", "codex": "hook"}
+    apply_inject_via_overlay(
+        config,
+        {"cursor": "hook", "claude": "hook", "codex": "hook"},
+    )
     config["tools"]["hook"]["tools_from"] = ["cloudflare"]
     config["tools"]["hook"]["cloudflare_url"] = ""