code-agnostic 0.3.4__tar.gz → 0.3.5__tar.gz

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: code-agnostic
-Version: 0.3.4
+Version: 0.3.5
 Summary: Centralized hub for LLM coding config: MCP, skills, rules, and agents.
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -36,11 +36,17 @@ AI coding tools each want config in a different place and format. When you use m
 ├── config/
 │   └── mcp.base.json             MCP servers (editor-agnostic)
 ├── rules/
-│   └── python-style.md           Rules with YAML frontmatter
+│   └── python-style/
+│       ├── meta.yaml             Rule metadata
+│       └── prompt.md             Rule instructions
 ├── skills/
-│   └── code-reviewer/SKILL.md    Skills with YAML frontmatter
+│   └── code-reviewer/
+│       ├── meta.yaml             Skill metadata
+│       └── prompt.md             Skill instructions
 └── agents/
-    └── architect.md              Agents with YAML frontmatter
+    └── architect/
+        ├── meta.yaml             Agent metadata
+        └── prompt.md             Agent instructions
 
         ↓ plan / apply ↓
 
@@ -51,6 +57,8 @@ AI coding tools each want config in a different place and format. When you use m
 
 Each resource is cross-compiled to the target editor's native format. Rules become `.mdc` files for Cursor, `AGENTS.md` sections for OpenCode/Codex, etc.
 
+Legacy single-file rules, `skills/<name>/SKILL.md`, and markdown agents are still supported for migration, but bundle directories are the preferred source format for new config.
+
 Today the implementation is still mixed: some assets are compiled and some are symlinked. The active migration plan is to move to generated outputs everywhere with a strict compiler contract instead of implicit per-app behavior.
 
 ## Install
@@ -88,6 +96,7 @@ code-agnostic apps enable -a cursor
 code-agnostic apps enable -a opencode
 
 # Preview and apply
+code-agnostic validate
 code-agnostic plan
 code-agnostic apply
 ```
@@ -103,7 +112,7 @@ code-agnostic apply
 | Workspace root `AGENTS.md` link | yes | yes | yes |
 | Native repo config include for workspace `AGENTS.md` | yes | -- | -- |
 | Repo/subdir gets shared workspace `AGENTS.md` today | yes | -- | yes |
-| Root-level `AGENTS.md` discovery only | -- | yes | yes |
+| Nested `AGENTS.md` discovery | -- | yes | yes |
 | Workspace propagation | yes | -- | yes |
 | Import from | yes | yes | yes |
 | Interactive import (TUI) | yes | yes | yes |
@@ -112,7 +121,7 @@ Cursor workspace propagation is intentionally disabled to avoid duplicate MCP in
 
 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`.
 
-Cursor documents `AGENTS.md` as a root-level project file. Codex documents `AGENTS.md` discovery, but not a native config include for an extra workspace file. In practice that means subdirectories and repos opened below the workspace root will not reliably get the shared workspace `AGENTS.md` today for Cursor.
+Cursor documents `AGENTS.md` support in project roots and subdirectories. `code-agnostic` still disables Cursor workspace propagation, so it 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.
 
 ## Features
 
@@ -121,12 +130,20 @@ Cursor documents `AGENTS.md` as a root-level project file. Codex documents `AGEN
 Plan-then-apply workflow. Preview every change before it touches disk.
 
 ```bash
+code-agnostic validate              # check canonical source files
 code-agnostic plan -a cursor        # dry-run for one editor
 code-agnostic plan                   # dry-run for all
 code-agnostic apply                  # apply changes
 code-agnostic status                 # check drift
 ```
 
+If managed outputs need repair after an apply, restore the active synced revision:
+
+```bash
+code-agnostic restore
+code-agnostic restore -w myproject
+```
+
 ### MCP management
 
 Add, remove, and list MCP servers without editing JSON by hand.
@@ -162,13 +179,32 @@ code-agnostic rules remove --name python-style
 
 ### Skills and agents
 
-Canonical YAML frontmatter format, cross-compiled per editor.
+Canonical YAML frontmatter format, cross-compiled per editor. Install or edit skills in the `code-agnostic` source of truth, then run `plan` / `apply`; do not hand-copy generated skills into `.codex`, `.cursor`, or OpenCode directories.
 
 ```bash
 code-agnostic skills list
 code-agnostic agents list
 ```
 
+Manual skill install today:
+
+```bash
+mkdir -p ~/.config/code-agnostic/skills
+cp -R ./my-skill ~/.config/code-agnostic/skills/my-skill
+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`.
+
+Planned convenience command:
+
+```bash
+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.
+
 ### 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`. Repo-local app config, skills, and agents are propagated for OpenCode and Codex.
@@ -210,13 +246,12 @@ All commands use named flags (`-a`, `-w`, `-v`). Singular aliases work too: `app
 
 The compiler migration is documented in:
 
-- [ROADMAP.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/ROADMAP.md)
-- [docs/compiler/overview.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/overview.md)
-- [docs/compiler/skills.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/skills.md)
-- [docs/compiler/agents.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/agents.md)
-- [docs/compiler/rules.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/rules.md)
-- [docs/compiler/mcp.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/mcp.md)
-- [docs/compiler/lossiness.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/lossiness.md)
+- [docs/compiler/overview.md](docs/compiler/overview.md)
+- [docs/compiler/skills.md](docs/compiler/skills.md)
+- [docs/compiler/agents.md](docs/compiler/agents.md)
+- [docs/compiler/rules.md](docs/compiler/rules.md)
+- [docs/compiler/mcp.md](docs/compiler/mcp.md)
+- [docs/compiler/lossiness.md](docs/compiler/lossiness.md)
 
 ## Roadmap
 
@@ -243,3 +278,11 @@ The compiler migration is documented in:
 uv sync --dev
 uv run pytest
 ```
+
+Real app-ingestion E2E is gated because it requires installed target CLIs and
+uses each tool's own introspection surface:
+
+```bash
+CODE_AGNOSTIC_REAL_APP_E2E=1 uv run pytest tests/e2e/test_real_app_ingestion_e2e.py -q
+CODE_AGNOSTIC_REAL_APP_E2E=1 CODE_AGNOSTIC_REAL_APP_TARGETS=codex,opencode uv run pytest tests/e2e/test_real_app_ingestion_e2e.py -q
+```

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/README.md

@@ -13,11 +13,17 @@ AI coding tools each want config in a different place and format. When you use m
 ├── config/
 │   └── mcp.base.json             MCP servers (editor-agnostic)
 ├── rules/
-│   └── python-style.md           Rules with YAML frontmatter
+│   └── python-style/
+│       ├── meta.yaml             Rule metadata
+│       └── prompt.md             Rule instructions
 ├── skills/
-│   └── code-reviewer/SKILL.md    Skills with YAML frontmatter
+│   └── code-reviewer/
+│       ├── meta.yaml             Skill metadata
+│       └── prompt.md             Skill instructions
 └── agents/
-    └── architect.md              Agents with YAML frontmatter
+    └── architect/
+        ├── meta.yaml             Agent metadata
+        └── prompt.md             Agent instructions
 
         ↓ plan / apply ↓
 
@@ -28,6 +34,8 @@ AI coding tools each want config in a different place and format. When you use m
 
 Each resource is cross-compiled to the target editor's native format. Rules become `.mdc` files for Cursor, `AGENTS.md` sections for OpenCode/Codex, etc.
 
+Legacy single-file rules, `skills/<name>/SKILL.md`, and markdown agents are still supported for migration, but bundle directories are the preferred source format for new config.
+
 Today the implementation is still mixed: some assets are compiled and some are symlinked. The active migration plan is to move to generated outputs everywhere with a strict compiler contract instead of implicit per-app behavior.
 
 ## Install
@@ -65,6 +73,7 @@ code-agnostic apps enable -a cursor
 code-agnostic apps enable -a opencode
 
 # Preview and apply
+code-agnostic validate
 code-agnostic plan
 code-agnostic apply
 ```
@@ -80,7 +89,7 @@ code-agnostic apply
 | Workspace root `AGENTS.md` link | yes | yes | yes |
 | Native repo config include for workspace `AGENTS.md` | yes | -- | -- |
 | Repo/subdir gets shared workspace `AGENTS.md` today | yes | -- | yes |
-| Root-level `AGENTS.md` discovery only | -- | yes | yes |
+| Nested `AGENTS.md` discovery | -- | yes | yes |
 | Workspace propagation | yes | -- | yes |
 | Import from | yes | yes | yes |
 | Interactive import (TUI) | yes | yes | yes |
@@ -89,7 +98,7 @@ Cursor workspace propagation is intentionally disabled to avoid duplicate MCP in
 
 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`.
 
-Cursor documents `AGENTS.md` as a root-level project file. Codex documents `AGENTS.md` discovery, but not a native config include for an extra workspace file. In practice that means subdirectories and repos opened below the workspace root will not reliably get the shared workspace `AGENTS.md` today for Cursor.
+Cursor documents `AGENTS.md` support in project roots and subdirectories. `code-agnostic` still disables Cursor workspace propagation, so it 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.
 
 ## Features
 
@@ -98,12 +107,20 @@ Cursor documents `AGENTS.md` as a root-level project file. Codex documents `AGEN
 Plan-then-apply workflow. Preview every change before it touches disk.
 
 ```bash
+code-agnostic validate              # check canonical source files
 code-agnostic plan -a cursor        # dry-run for one editor
 code-agnostic plan                   # dry-run for all
 code-agnostic apply                  # apply changes
 code-agnostic status                 # check drift
 ```
 
+If managed outputs need repair after an apply, restore the active synced revision:
+
+```bash
+code-agnostic restore
+code-agnostic restore -w myproject
+```
+
 ### MCP management
 
 Add, remove, and list MCP servers without editing JSON by hand.
@@ -139,13 +156,32 @@ code-agnostic rules remove --name python-style
 
 ### Skills and agents
 
-Canonical YAML frontmatter format, cross-compiled per editor.
+Canonical YAML frontmatter format, cross-compiled per editor. Install or edit skills in the `code-agnostic` source of truth, then run `plan` / `apply`; do not hand-copy generated skills into `.codex`, `.cursor`, or OpenCode directories.
 
 ```bash
 code-agnostic skills list
 code-agnostic agents list
 ```
 
+Manual skill install today:
+
+```bash
+mkdir -p ~/.config/code-agnostic/skills
+cp -R ./my-skill ~/.config/code-agnostic/skills/my-skill
+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`.
+
+Planned convenience command:
+
+```bash
+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.
+
 ### 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`. Repo-local app config, skills, and agents are propagated for OpenCode and Codex.
@@ -187,13 +223,12 @@ All commands use named flags (`-a`, `-w`, `-v`). Singular aliases work too: `app
 
 The compiler migration is documented in:
 
-- [ROADMAP.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/ROADMAP.md)
-- [docs/compiler/overview.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/overview.md)
-- [docs/compiler/skills.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/skills.md)
-- [docs/compiler/agents.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/agents.md)
-- [docs/compiler/rules.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/rules.md)
-- [docs/compiler/mcp.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/mcp.md)
-- [docs/compiler/lossiness.md](/Users/alexeyartishevsky/PycharmProjects/llm-sync/docs/compiler/lossiness.md)
+- [docs/compiler/overview.md](docs/compiler/overview.md)
+- [docs/compiler/skills.md](docs/compiler/skills.md)
+- [docs/compiler/agents.md](docs/compiler/agents.md)
+- [docs/compiler/rules.md](docs/compiler/rules.md)
+- [docs/compiler/mcp.md](docs/compiler/mcp.md)
+- [docs/compiler/lossiness.md](docs/compiler/lossiness.md)
 
 ## Roadmap
 
@@ -220,3 +255,11 @@ The compiler migration is documented in:
 uv sync --dev
 uv run pytest
 ```
+
+Real app-ingestion E2E is gated because it requires installed target CLIs and
+uses each tool's own introspection surface:
+
+```bash
+CODE_AGNOSTIC_REAL_APP_E2E=1 uv run pytest tests/e2e/test_real_app_ingestion_e2e.py -q
+CODE_AGNOSTIC_REAL_APP_E2E=1 CODE_AGNOSTIC_REAL_APP_TARGETS=codex,opencode uv run pytest tests/e2e/test_real_app_ingestion_e2e.py -q
+```

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/code_agnostic/__init__.py

@@ -1,3 +1,3 @@
 __all__ = ["__version__"]
 
-__version__ = "0.1.0"
+__version__ = "0.3.5"

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/code_agnostic/__main__.py

@@ -48,13 +48,15 @@ cli.add_command(import_group)
 
 def main() -> int:
     try:
-        cli(standalone_mode=False)
+        result = cli(standalone_mode=False)
     except click.exceptions.Exit as exc:
         code = exc.exit_code
         return code if isinstance(code, int) else 1
     except click.ClickException as exc:
         exc.show()
         return 2
+    if isinstance(result, int):
+        return result
     return 0
 
 

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/code_agnostic/agents/opencode.py

@@ -22,25 +22,25 @@ def serialize_opencode_agent(agent: Agent) -> str:
     if reasoning_effort:
         fm["reasoningEffort"] = reasoning_effort
 
-    tools: dict[str, Any] = {}
-    if agent.metadata.tools.read is not True:
-        tools["read"] = agent.metadata.tools.read
-    if agent.metadata.tools.write is not True:
-        tools["write"] = agent.metadata.tools.write
-    if agent.metadata.tools.mcp:
-        tools["mcp"] = agent.metadata.tools.mcp
-    if tools:
-        fm["tools"] = tools
-
-    for key, value in agent.metadata.app_passthrough(
+    passthrough = agent.metadata.app_passthrough(
         "opencode",
         consumed_keys={
             "model",
             "reasoning_effort",
             "sandbox_mode",
             "nickname_candidates",
+            "permission",
         },
-    ).items():
+    )
+
+    permission = _merge_permission(
+        _compile_permission(agent),
+        agent.metadata.app_overrides.get("opencode", {}).get("permission"),
+    )
+    if permission:
+        fm["permission"] = permission
+
+    for key, value in passthrough.items():
         if key in fm:
             continue
         fm[key] = value
@@ -54,3 +54,27 @@ def serialize_opencode_agent(agent: Agent) -> str:
 
     parts.append(agent.content)
     return "\n".join(parts)
+
+
+def _compile_permission(agent: Agent) -> dict[str, Any]:
+    permission: dict[str, Any] = {}
+    permission["read"] = "allow" if agent.metadata.tools.read else "deny"
+    permission["edit"] = "allow" if agent.metadata.tools.write else "deny"
+    for item in agent.metadata.tools.mcp:
+        server = item.get("server")
+        if not server:
+            continue
+        tool = item.get("tool")
+        key = f"{server}_{tool}" if tool else f"{server}_*"
+        permission[key] = "allow"
+    return permission
+
+
+def _merge_permission(
+    generated: dict[str, Any], override: Any | None
+) -> dict[str, Any] | Any:
+    if override is None:
+        return generated
+    if isinstance(override, dict):
+        return {**generated, **override}
+    return override

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/code_agnostic/apps/app_id.py

@@ -60,7 +60,7 @@ APP_CATALOG: dict[AppId, AppMetadata] = {
         toggleable=True,
         importable=True,
         supports_import_agents=True,
-        supports_workspace_propagation=True,
+        supports_workspace_propagation=False,
         project_dir_name=CURSOR_PROJECT_DIRNAME,
         config_filename=CURSOR_CONFIG_FILENAME,
     ),

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/code_agnostic/apps/apps_service.py

@@ -86,6 +86,9 @@ class AppsService:
 
     def plan_for_target(self, target: str) -> SyncPlan:
         normalized = target.lower()
+        if normalized != "all" and not self.is_enabled(normalized):
+            return SyncPlan([], [], [f"{normalized} is disabled for sync."])
+
         app_services = self._resolve_services_for_target(normalized)
         plan = SyncPlanner(
             core=self.core_repository,

{code_agnostic-0.3.4 → code_agnostic-0.3.5}/code_agnostic/apps/codex/config_repository.py

@@ -11,6 +11,7 @@ import tomlkit
 from code_agnostic.apps.common.interfaces.repositories import IAppConfigRepository
 from code_agnostic.constants import (
     AGENTS_DIRNAME,
+    AGENTS_PROJECT_DIRNAME,
     CODEX_CONFIG_FILENAME,
     CODEX_PROJECT_DIRNAME,
     SKILLS_DIRNAME,
@@ -32,7 +33,7 @@ class CodexConfigRepository(IAppConfigRepository):
 
     @property
     def skills_dir(self) -> Path:
-        return self.root / SKILLS_DIRNAME
+        return self.root.parent / AGENTS_PROJECT_DIRNAME / SKILLS_DIRNAME
 
     @property
     def agents_dir(self) -> Path: