code-agnostic 0.3.11__tar.gz → 0.3.13__tar.gz

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: code-agnostic
-Version: 0.3.11
+Version: 0.3.13
 Summary: Centralized hub for LLM coding config: MCP, skills, rules, and agents.
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -54,7 +54,7 @@ AI coding tools each want config in a different place and format. When you use m
 
 ~/.config/opencode/               Compiled & synced for OpenCode
 ~/.cursor/                        Compiled & synced for Cursor
-~/.codex/                         Compiled & synced for Codex
+~/.codex/                         Compiled & synced for Codex (or CODEX_HOME)
 ~/.claude.json and ~/.claude/      Compiled & synced for Claude Code
 ```
 
@@ -66,18 +66,19 @@ Today the implementation is still mixed: some assets are compiled and some are s
 
 ## Scope model
 
-`code-agnostic` has two managed source scopes today:
+`code-agnostic` has three managed source scopes:
 
 - global source config under `~/.config/code-agnostic/`, synced to enabled
   user-level app config;
 - workspace source config under `~/.config/code-agnostic/workspaces/<name>/`,
-  propagated into repos inside a registered workspace.
+  propagated into repos inside a registered workspace;
+- project source config under `~/.config/code-agnostic/projects/<name>/`,
+  synced to exactly one registered project directory.
 
-Project-local skill folders that users create directly inside a repo, such as
-`.agents/skills` or `.opencode/skills`, are app-native inputs but are not
-managed as source by `code-agnostic` yet. First-class project-scoped installs
-are planned so a single registered project can have managed local source config
-without bypassing the hub.
+Workspace sync may generate repo-local outputs, but those outputs are not
+source. Project-local skill folders generated inside a repo, such as
+`.agents/skills` or `.opencode/skills`, are also generated outputs; install
+skills into managed project source first, then run `plan` / `apply`.
 
 ## Install
 
@@ -142,9 +143,9 @@ that are omitted or rejected for a selected target.
 
 Cursor workspace propagation writes repo-local MCP, skills, and agents when those resources exist in the workspace source config.
 
-OpenCode workspace configs include the shared workspace `AGENTS.md` natively via `instructions`, so repos under the workspace get both repo-local and shared workspace instructions. Codex repos receive workspace instructions through a generated `AGENTS.override.md`, which is added to each repo's `.git/info/exclude`. Claude Code receives workspace instructions through generated `CLAUDE.local.md` files, never by editing committed `CLAUDE.md`.
+OpenCode workspace configs write project-root `opencode.json` files that include the shared workspace `AGENTS.md` natively via `instructions`, so repos under the workspace get both repo-local and shared workspace instructions. Codex repos receive workspace instructions through a generated `AGENTS.override.md`, which is added to each repo's `.git/info/exclude`. Claude Code receives workspace instructions through generated `CLAUDE.local.md` files, never by editing committed `CLAUDE.md`.
 
-Cursor documents `AGENTS.md` support in project roots and subdirectories. `code-agnostic` does not copy or link the shared workspace `AGENTS.md` into child repos; Cursor will load repo-local or nested `AGENTS.md` files that already exist in the opened project. Codex documents nested `AGENTS.md` discovery, but not a native config include for an extra workspace file.
+Cursor documents `AGENTS.md` support in project roots and subdirectories. `code-agnostic` does not copy or link the shared workspace `AGENTS.md` into child repos; Cursor will load `AGENTS.md` files that already exist in the opened project. Codex documents nested `AGENTS.md` discovery, but not a native config include for an extra workspace file.
 
 ## Features
 
@@ -229,16 +230,27 @@ code-agnostic skills list
 code-agnostic agents list
 ```
 
-Manual skill install today:
+Install a local skill directory into managed source:
 
 ```bash
-mkdir -p ~/.config/code-agnostic/skills
-cp -R ./my-skill ~/.config/code-agnostic/skills/my-skill
+code-agnostic skills install ./my-skill --global
+code-agnostic skills install ./my-skill --workspace myworkspace
+code-agnostic projects add --name myproject --path .
+code-agnostic skills install ./my-skill --project myproject
 code-agnostic plan
 code-agnostic apply
 ```
 
-Global skills live under `~/.config/code-agnostic/skills`. Workspace-local skills live under `~/.config/code-agnostic/workspaces/<name>/skills` and can be inspected with `code-agnostic skills list -w <name>`. Codex generated skill outputs are written to `~/.agents/skills`, while Codex agents and config remain under `~/.codex`. Claude Code generated skills and agents are written under `~/.claude/skills` and `~/.claude/agents`, with workspace copies under repo-local `.claude/skills` and `.claude/agents`.
+Global skills live under `~/.config/code-agnostic/skills`. Workspace-local
+skills live under `~/.config/code-agnostic/workspaces/<name>/skills` and can be
+inspected with `code-agnostic skills list -w <name>`. Project-local skills live
+under `~/.config/code-agnostic/projects/<name>/skills` and are generated into
+the registered project directory by `plan` / `apply`. Codex generated skill
+outputs are written to `~/.agents/skills`, while Codex agents and config remain
+under `CODEX_HOME` when set, defaulting to `~/.codex`. Claude Code generated
+skills and agents are written under `~/.claude/skills` and `~/.claude/agents`,
+with workspace/project copies under repo-local `.claude/skills` and
+`.claude/agents`.
 
 Project-local skills are not first-class source inputs in `code-agnostic` yet. If a target app discovers repo-local skill folders such as `.agents/skills`, `.opencode/skills`, or user-created `.claude/skills`, treat those as unmanaged app inputs. Workspace sync writes only the exact generated paths recorded in `.sync-state.json`.
 
@@ -249,10 +261,12 @@ code-agnostic skills install ./my-skill --apply
 ```
 
 That command should copy the skill into the source of truth and then run the normal compiler/apply flow.
+See [docs/project-scoped-skills.md](docs/project-scoped-skills.md) for the
+first implementation slice.
 
 ### Workspaces
 
-Register workspace directories. Workspace rules are compiled into a canonical `AGENTS.md` at the workspace root. Repos keep their own repo-specific `AGENTS.md`; Codex receives the workspace rules through generated, git-excluded `AGENTS.override.md` files, while OpenCode workspace configs reference the shared workspace file through `instructions`. Claude receives generated `CLAUDE.local.md` files and project MCP entries in `~/.claude.json["projects"][absolute_repo_path]["mcpServers"]`. Workspace source config, skills, and agents are propagated into repo-local generated paths for OpenCode, Cursor, Codex, and Claude; user-created project-local skill folders remain unmanaged until project-scoped installs are supported.
+Register workspace directories. Workspace rules are compiled into a canonical `AGENTS.md` at the workspace root. Repos keep their own repo-specific `AGENTS.md`; Codex receives the workspace rules through generated, git-excluded `AGENTS.override.md` files, while OpenCode workspace configs write project-root `opencode.json` files that reference the shared workspace file through `instructions`. Claude receives generated `CLAUDE.local.md` files and project MCP entries in `~/.claude.json["projects"][absolute_repo_path]["mcpServers"]`. Workspace source config, skills, and agents are propagated into repo-local generated paths for OpenCode, Cursor, Codex, and Claude; user-created project-local skill folders remain unmanaged until project-scoped installs are supported.
 
 Cursor propagation intentionally stays to repo-local MCP, skills, and agents; it does not copy the shared workspace `AGENTS.md` into child repos.
 
@@ -316,12 +330,12 @@ The compiler migration is documented in:
 - [x] MCP add/remove/list commands
 - [x] Rules system with YAML frontmatter and per-editor compilation
 - [x] Cross-compilation for skills and agents
+- [x] Planner integration for cross-compiled skills and agents
 - [x] Per-workspace git-exclude customization
 - [x] Interactive TUI for import selection
 - [x] Claude Code support
 - [ ] Project-scoped skill installs and sync
 - [ ] `rules add` / `skills add` / `agents add` commands (open `$EDITOR` with template)
-- [ ] Planner integration for cross-compiled skills and agents
 - [ ] Shell auto-complete
 - [ ] Full TUI mode (command palette + menus)
 

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/README.md

@@ -29,7 +29,7 @@ AI coding tools each want config in a different place and format. When you use m
 
 ~/.config/opencode/               Compiled & synced for OpenCode
 ~/.cursor/                        Compiled & synced for Cursor
-~/.codex/                         Compiled & synced for Codex
+~/.codex/                         Compiled & synced for Codex (or CODEX_HOME)
 ~/.claude.json and ~/.claude/      Compiled & synced for Claude Code
 ```
 
@@ -41,18 +41,19 @@ Today the implementation is still mixed: some assets are compiled and some are s
 
 ## Scope model
 
-`code-agnostic` has two managed source scopes today:
+`code-agnostic` has three managed source scopes:
 
 - global source config under `~/.config/code-agnostic/`, synced to enabled
   user-level app config;
 - workspace source config under `~/.config/code-agnostic/workspaces/<name>/`,
-  propagated into repos inside a registered workspace.
+  propagated into repos inside a registered workspace;
+- project source config under `~/.config/code-agnostic/projects/<name>/`,
+  synced to exactly one registered project directory.
 
-Project-local skill folders that users create directly inside a repo, such as
-`.agents/skills` or `.opencode/skills`, are app-native inputs but are not
-managed as source by `code-agnostic` yet. First-class project-scoped installs
-are planned so a single registered project can have managed local source config
-without bypassing the hub.
+Workspace sync may generate repo-local outputs, but those outputs are not
+source. Project-local skill folders generated inside a repo, such as
+`.agents/skills` or `.opencode/skills`, are also generated outputs; install
+skills into managed project source first, then run `plan` / `apply`.
 
 ## Install
 
@@ -117,9 +118,9 @@ that are omitted or rejected for a selected target.
 
 Cursor workspace propagation writes repo-local MCP, skills, and agents when those resources exist in the workspace source config.
 
-OpenCode workspace configs include the shared workspace `AGENTS.md` natively via `instructions`, so repos under the workspace get both repo-local and shared workspace instructions. Codex repos receive workspace instructions through a generated `AGENTS.override.md`, which is added to each repo's `.git/info/exclude`. Claude Code receives workspace instructions through generated `CLAUDE.local.md` files, never by editing committed `CLAUDE.md`.
+OpenCode workspace configs write project-root `opencode.json` files that include the shared workspace `AGENTS.md` natively via `instructions`, so repos under the workspace get both repo-local and shared workspace instructions. Codex repos receive workspace instructions through a generated `AGENTS.override.md`, which is added to each repo's `.git/info/exclude`. Claude Code receives workspace instructions through generated `CLAUDE.local.md` files, never by editing committed `CLAUDE.md`.
 
-Cursor documents `AGENTS.md` support in project roots and subdirectories. `code-agnostic` does not copy or link the shared workspace `AGENTS.md` into child repos; Cursor will load repo-local or nested `AGENTS.md` files that already exist in the opened project. Codex documents nested `AGENTS.md` discovery, but not a native config include for an extra workspace file.
+Cursor documents `AGENTS.md` support in project roots and subdirectories. `code-agnostic` does not copy or link the shared workspace `AGENTS.md` into child repos; Cursor will load `AGENTS.md` files that already exist in the opened project. Codex documents nested `AGENTS.md` discovery, but not a native config include for an extra workspace file.
 
 ## Features
 
@@ -204,16 +205,27 @@ code-agnostic skills list
 code-agnostic agents list
 ```
 
-Manual skill install today:
+Install a local skill directory into managed source:
 
 ```bash
-mkdir -p ~/.config/code-agnostic/skills
-cp -R ./my-skill ~/.config/code-agnostic/skills/my-skill
+code-agnostic skills install ./my-skill --global
+code-agnostic skills install ./my-skill --workspace myworkspace
+code-agnostic projects add --name myproject --path .
+code-agnostic skills install ./my-skill --project myproject
 code-agnostic plan
 code-agnostic apply
 ```
 
-Global skills live under `~/.config/code-agnostic/skills`. Workspace-local skills live under `~/.config/code-agnostic/workspaces/<name>/skills` and can be inspected with `code-agnostic skills list -w <name>`. Codex generated skill outputs are written to `~/.agents/skills`, while Codex agents and config remain under `~/.codex`. Claude Code generated skills and agents are written under `~/.claude/skills` and `~/.claude/agents`, with workspace copies under repo-local `.claude/skills` and `.claude/agents`.
+Global skills live under `~/.config/code-agnostic/skills`. Workspace-local
+skills live under `~/.config/code-agnostic/workspaces/<name>/skills` and can be
+inspected with `code-agnostic skills list -w <name>`. Project-local skills live
+under `~/.config/code-agnostic/projects/<name>/skills` and are generated into
+the registered project directory by `plan` / `apply`. Codex generated skill
+outputs are written to `~/.agents/skills`, while Codex agents and config remain
+under `CODEX_HOME` when set, defaulting to `~/.codex`. Claude Code generated
+skills and agents are written under `~/.claude/skills` and `~/.claude/agents`,
+with workspace/project copies under repo-local `.claude/skills` and
+`.claude/agents`.
 
 Project-local skills are not first-class source inputs in `code-agnostic` yet. If a target app discovers repo-local skill folders such as `.agents/skills`, `.opencode/skills`, or user-created `.claude/skills`, treat those as unmanaged app inputs. Workspace sync writes only the exact generated paths recorded in `.sync-state.json`.
 
@@ -224,10 +236,12 @@ code-agnostic skills install ./my-skill --apply
 ```
 
 That command should copy the skill into the source of truth and then run the normal compiler/apply flow.
+See [docs/project-scoped-skills.md](docs/project-scoped-skills.md) for the
+first implementation slice.
 
 ### Workspaces
 
-Register workspace directories. Workspace rules are compiled into a canonical `AGENTS.md` at the workspace root. Repos keep their own repo-specific `AGENTS.md`; Codex receives the workspace rules through generated, git-excluded `AGENTS.override.md` files, while OpenCode workspace configs reference the shared workspace file through `instructions`. Claude receives generated `CLAUDE.local.md` files and project MCP entries in `~/.claude.json["projects"][absolute_repo_path]["mcpServers"]`. Workspace source config, skills, and agents are propagated into repo-local generated paths for OpenCode, Cursor, Codex, and Claude; user-created project-local skill folders remain unmanaged until project-scoped installs are supported.
+Register workspace directories. Workspace rules are compiled into a canonical `AGENTS.md` at the workspace root. Repos keep their own repo-specific `AGENTS.md`; Codex receives the workspace rules through generated, git-excluded `AGENTS.override.md` files, while OpenCode workspace configs write project-root `opencode.json` files that reference the shared workspace file through `instructions`. Claude receives generated `CLAUDE.local.md` files and project MCP entries in `~/.claude.json["projects"][absolute_repo_path]["mcpServers"]`. Workspace source config, skills, and agents are propagated into repo-local generated paths for OpenCode, Cursor, Codex, and Claude; user-created project-local skill folders remain unmanaged until project-scoped installs are supported.
 
 Cursor propagation intentionally stays to repo-local MCP, skills, and agents; it does not copy the shared workspace `AGENTS.md` into child repos.
 
@@ -291,12 +305,12 @@ The compiler migration is documented in:
 - [x] MCP add/remove/list commands
 - [x] Rules system with YAML frontmatter and per-editor compilation
 - [x] Cross-compilation for skills and agents
+- [x] Planner integration for cross-compiled skills and agents
 - [x] Per-workspace git-exclude customization
 - [x] Interactive TUI for import selection
 - [x] Claude Code support
 - [ ] Project-scoped skill installs and sync
 - [ ] `rules add` / `skills add` / `agents add` commands (open `$EDITOR` with template)
-- [ ] Planner integration for cross-compiled skills and agents
 - [ ] Shell auto-complete
 - [ ] Full TUI mode (command palette + menus)
 

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/__init__.py

@@ -1,3 +1,3 @@
 __all__ = ["__version__"]
 
-__version__ = "0.3.11"
+__version__ = "0.3.13"

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/__main__.py

@@ -10,6 +10,7 @@ from code_agnostic.cli.commands.explain_lossiness import explain_lossiness
 from code_agnostic.cli.commands.import_ import import_group
 from code_agnostic.cli.commands.mcp import mcp
 from code_agnostic.cli.commands.plan import plan
+from code_agnostic.cli.commands.projects import projects
 from code_agnostic.cli.commands.restore import restore
 from code_agnostic.cli.commands.rules import rules
 from code_agnostic.cli.commands.skills import skills
@@ -25,7 +26,7 @@ from code_agnostic.errors import SyncAppError
 )
 @click.pass_context
 def cli(ctx: click.Context) -> None:
-    """App-based config sync."""
+    """Manage one source of truth for AI coding-tool config."""
     ctx.obj = {}
 
 
@@ -40,6 +41,7 @@ cli.add_command(explain_lossiness)
 # Register command groups
 cli.add_command(apps)
 cli.add_command(workspaces)
+cli.add_command(projects)
 cli.add_command(rules)
 cli.add_command(skills)
 cli.add_command(agents_group)

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/agents/opencode.py

@@ -7,14 +7,19 @@ from typing import Any
 import yaml
 
 from code_agnostic.agents.models import Agent
+from code_agnostic.errors import InvalidConfigSchemaError
 
 
 def serialize_opencode_agent(agent: Agent) -> str:
     fm: dict[str, Any] = {}
     if agent.metadata.name:
         fm["name"] = agent.metadata.name
-    if agent.metadata.description:
-        fm["description"] = agent.metadata.description
+    if not agent.metadata.description:
+        raise InvalidConfigSchemaError(
+            agent.source_path,
+            "OpenCode agents require a description",
+        )
+    fm["description"] = agent.metadata.description
     model = agent.metadata.effective_value("opencode", "model")
     if model:
         fm["model"] = model

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/apps/codex/config_repository.py

@@ -1,3 +1,4 @@
+import os
 from pathlib import Path
 from typing import Any
 
@@ -21,7 +22,8 @@ from code_agnostic.errors import InvalidConfigSchemaError, InvalidJsonFormatErro
 
 class CodexConfigRepository(IAppConfigRepository):
     def __init__(self, root: Path | None = None) -> None:
-        self._root = root or (Path.home() / CODEX_PROJECT_DIRNAME)
+        self._root = root or _default_codex_root()
+        self._skills_dir = _default_codex_skills_dir(root)
 
     @property
     def root(self) -> Path:
@@ -33,7 +35,7 @@ class CodexConfigRepository(IAppConfigRepository):
 
     @property
     def skills_dir(self) -> Path:
-        return self.root.parent / AGENTS_PROJECT_DIRNAME / SKILLS_DIRNAME
+        return self._skills_dir
 
     @property
     def agents_dir(self) -> Path:
@@ -81,3 +83,16 @@ class CodexConfigRepository(IAppConfigRepository):
         config = self.load_config()
         config["agents"] = payload
         self.save_config(config)
+
+
+def _default_codex_root() -> Path:
+    codex_home = os.environ.get("CODEX_HOME")
+    if codex_home:
+        return Path(codex_home).expanduser()
+    return Path.home() / CODEX_PROJECT_DIRNAME
+
+
+def _default_codex_skills_dir(root: Path | None) -> Path:
+    if root is not None:
+        return root.parent / AGENTS_PROJECT_DIRNAME / SKILLS_DIRNAME
+    return Path.home() / AGENTS_PROJECT_DIRNAME / SKILLS_DIRNAME

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/apps/codex/schema.json

@@ -226,18 +226,6 @@
       },
       "type": "object"
     },
-    "AppsMcpPathOverrideConfigToml": {
-      "additionalProperties": false,
-      "properties": {
-        "enabled": {
-          "type": "boolean"
-        },
-        "path": {
-          "type": "string"
-        }
-      },
-      "type": "object"
-    },
     "AskForApproval": {
       "description": "Determines the conditions under which the user is consulted to approve running the command proposed by Codex.",
       "oneOf": [
@@ -408,7 +396,23 @@
               "type": "boolean"
             },
             "apps_mcp_path_override": {
-              "$ref": "#/definitions/FeatureToml_for_AppsMcpPathOverrideConfigToml"
+              "anyOf": [
+                {
+                  "type": "boolean"
+                },
+                {
+                  "additionalProperties": false,
+                  "properties": {
+                    "enabled": {
+                      "type": "boolean"
+                    },
+                    "path": {
+                      "type": "string"
+                    }
+                  },
+                  "type": "object"
+                }
+              ]
             },
             "auth_elicitation": {
               "type": "boolean"
@@ -836,16 +840,6 @@
       },
       "type": "object"
     },
-    "FeatureToml_for_AppsMcpPathOverrideConfigToml": {
-      "anyOf": [
-        {
-          "type": "boolean"
-        },
-        {
-          "$ref": "#/definitions/AppsMcpPathOverrideConfigToml"
-        }
-      ]
-    },
     "FeatureToml_for_CodeModeConfigToml": {
       "anyOf": [
         {
@@ -4534,7 +4528,23 @@
           "type": "boolean"
         },
         "apps_mcp_path_override": {
-          "$ref": "#/definitions/FeatureToml_for_AppsMcpPathOverrideConfigToml"
+          "anyOf": [
+            {
+              "type": "boolean"
+            },
+            {
+              "additionalProperties": false,
+              "properties": {
+                "enabled": {
+                  "type": "boolean"
+                },
+                "path": {
+                  "type": "string"
+                }
+              },
+              "type": "object"
+            }
+          ]
         },
         "auth_elicitation": {
           "type": "boolean"

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/apps/opencode/config_repository.py

@@ -13,8 +13,15 @@ from code_agnostic.utils import merge_dict_overlay, read_json_safe, write_json
 
 
 class OpenCodeConfigRepository(IAppConfigRepository):
-    def __init__(self, root: Path | None = None) -> None:
+    def __init__(
+        self,
+        root: Path | None = None,
+        config_path: Path | None = None,
+        legacy_config_path: Path | None = None,
+    ) -> None:
         self._root = root or (Path.home() / ".config" / "opencode")
+        self._config_path = config_path
+        self._legacy_config_path = legacy_config_path
 
     @property
     def root(self) -> Path:
@@ -22,7 +29,7 @@ class OpenCodeConfigRepository(IAppConfigRepository):
 
     @property
     def config_path(self) -> Path:
-        return self.root / OPENCODE_CONFIG_FILENAME
+        return self._config_path or self.root / OPENCODE_CONFIG_FILENAME
 
     @property
     def skills_dir(self) -> Path:
@@ -39,13 +46,14 @@ class OpenCodeConfigRepository(IAppConfigRepository):
         return plural
 
     def load_config(self) -> dict[str, Any]:
-        payload, error = read_json_safe(self.config_path)
+        config_path = self._read_config_path()
+        payload, error = read_json_safe(config_path)
         if error is not None:
-            raise InvalidJsonFormatError(self.config_path, error)
+            raise InvalidJsonFormatError(config_path, error)
         if payload is None:
             return {}
         if not isinstance(payload, dict):
-            raise InvalidConfigSchemaError(self.config_path, "must be a JSON object")
+            raise InvalidConfigSchemaError(config_path, "must be a JSON object")
         return payload
 
     def save_config(self, payload: dict[str, Any]) -> None:
@@ -105,3 +113,8 @@ class OpenCodeConfigRepository(IAppConfigRepository):
 
         if tools:
             merged["tools"] = tools
+
+    def _read_config_path(self) -> Path:
+        if self.config_path.exists() or self._legacy_config_path is None:
+            return self.config_path
+        return self._legacy_config_path

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/apps/opencode/schema.json

@@ -43,48 +43,44 @@
       },
       "additionalProperties": false
     },
-    "ReferenceConfigEntry": {
-      "anyOf": [
-        {
+    "ConfigV2.Reference.Git": {
+      "type": "object",
+      "properties": {
+        "repository": {
           "type": "string"
         },
-        {
-          "type": "object",
-          "properties": {
-            "repository": {
-              "type": "string",
-              "description": "Git repository URL, host/path reference, or GitHub owner/repo shorthand"
-            },
-            "branch": {
-              "type": "string",
-              "description": "Branch or ref to clone and inspect"
-            }
-          },
-          "required": [
-            "repository"
-          ],
-          "additionalProperties": false
+        "branch": {
+          "type": "string"
         },
-        {
-          "type": "object",
-          "properties": {
-            "path": {
-              "type": "string",
-              "description": "Absolute path, ~/ path, or workspace-relative path to a local reference directory"
-            }
-          },
-          "required": [
-            "path"
-          ],
-          "additionalProperties": false
+        "description": {
+          "type": "string"
+        },
+        "hidden": {
+          "type": "boolean"
         }
-      ]
+      },
+      "required": [
+        "repository"
+      ],
+      "additionalProperties": false
     },
-    "ReferenceConfig": {
+    "ConfigV2.Reference.Local": {
       "type": "object",
-      "additionalProperties": {
-        "$ref": "#/$defs/ReferenceConfigEntry"
-      }
+      "properties": {
+        "path": {
+          "type": "string"
+        },
+        "description": {
+          "type": "string"
+        },
+        "hidden": {
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "path"
+      ],
+      "additionalProperties": false
     },
     "PermissionActionConfig": {
       "type": "string",
@@ -390,6 +386,7 @@
                       "field": {
                         "type": "string",
                         "enum": [
+                          "reasoning",
                           "reasoning_content",
                           "reasoning_details"
                         ]
@@ -826,9 +823,39 @@
           "additionalProperties": false,
           "description": "Additional skill folder paths"
         },
+        "references": {
+          "type": "object",
+          "additionalProperties": {
+            "anyOf": [
+              {
+                "type": "string"
+              },
+              {
+                "$ref": "#/$defs/ConfigV2.Reference.Git"
+              },
+              {
+                "$ref": "#/$defs/ConfigV2.Reference.Local"
+              }
+            ]
+          },
+          "description": "Named git or local directory references"
+        },
         "reference": {
-          "$ref": "#/$defs/ReferenceConfig",
-          "description": "Named git or local directory references that can be mentioned as @alias or @alias/path"
+          "type": "object",
+          "additionalProperties": {
+            "anyOf": [
+              {
+                "type": "string"
+              },
+              {
+                "$ref": "#/$defs/ConfigV2.Reference.Git"
+              },
+              {
+                "$ref": "#/$defs/ConfigV2.Reference.Local"
+              }
+            ]
+          },
+          "description": "@deprecated Use 'references' field instead. Named git or local directory references"
         },
         "watcher": {
           "type": "object",

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/cli/commands/agents.py

@@ -5,7 +5,7 @@ import shutil
 import click
 from rich.console import Console
 
-from code_agnostic.cli.helpers import workspace_config_root
+from code_agnostic.cli.helpers import validate_resource_name, workspace_config_root
 from code_agnostic.cli.options import workspace_option
 from code_agnostic.core.repository import CoreRepository
 from code_agnostic.tui import SyncConsoleUI
@@ -33,6 +33,7 @@ def agents_list(obj: dict[str, str], workspace: str | None) -> None:
 @workspace_option()
 @click.pass_obj
 def agents_remove(obj: dict[str, str], name: str, workspace: str | None) -> None:
+    validate_resource_name(name, "agent")
     core = CoreRepository()
     root = workspace_config_root(core, workspace)
     agent_dir = root / "agents" / name

{code_agnostic-0.3.11 → code_agnostic-0.3.13}/code_agnostic/cli/commands/apps.py

@@ -30,8 +30,10 @@ def apps_enable(obj: dict[str, str], app: str) -> None:
     ui = SyncConsoleUI(Console())
     core = CoreRepository()
     service = AppsService(core)
-    service.enable(app.lower())
+    app = app.lower()
+    service.enable(app)
     ui.render_apps(service.list_status_rows())
+    ui.render_app_enabled_next_steps(app)
 
 
 @apps.command("disable", help="Disable app sync target.")