oasr 0.4.1__tar.gz → 0.4.2__tar.gz

{oasr-0.4.1 → oasr-0.4.2}/CHANGELOG.md

@@ -4,6 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.2] - 2026-02-01
+
+### Added
+- **registry prune subcommand**: Added `oasr registry prune` to align with registry command taxonomy
+
+### Changed
+- **clean command**: Deprecated `oasr clean` in favor of `oasr registry prune` (will be removed in v0.6.0)
+- **documentation**: Updated REGISTRY.md with prune subcommand documentation and usage examples
+
 ## [0.4.1] - 2026-02-01
 
 ### Fixed

{oasr-0.4.1 → oasr-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: oasr
-Version: 0.4.1
+Version: 0.4.2
 Summary: CLI for managing agent skills across IDE integrations
 Project-URL: Homepage, https://github.com/jgodau/asr
 Project-URL: Repository, https://github.com/jgodau/asr

{oasr-0.4.1 → oasr-0.4.2}/docs/commands/.INDEX.md

@@ -3,7 +3,7 @@
 ## Core Commands (v0.4.0)
 
 - [oasr](ROOT.md) - Global flags and options
-- [oasr registry](REGISTRY.md) - Manage skill registry (validate, add, remove, list, sync)
+- [oasr registry](REGISTRY.md) - Manage skill registry (validate, add, remove, list, sync, prune)
 - [oasr diff](DIFF.md) - Show status of tracked skills
 - [oasr sync](SYNC.md) - Refresh outdated tracked skills
 - [oasr config](CONFIG.md) - Manage configuration (NEW in v0.4.0)
@@ -11,7 +11,6 @@
 - [oasr exec](EXEC.md) - Execute skills as CLI tools (NEW in v0.4.0)
 - [oasr find](FIND.md) - Find/discover skills in your file system
 - [oasr validate](VALIDATE.md) - Validate a skill
-- [oasr clean](CLEAN.md) - Clean up the registry
 - [oasr adapter](ADAPTER.md) - Generate IDE/Tooling adapters
 - [oasr update](UPDATE.md) - Update the `oasr` CLI
 - [oasr info](INFO.md) - Show detailed information about a skill
@@ -19,6 +18,9 @@
 
 ## Deprecated Commands
 
+### v0.4.1 Deprecations
+- [oasr clean](CLEAN.md) - **Deprecated**, use `oasr registry prune` instead (will be removed in v0.6.0)
+
 ### v0.4.0 Deprecations
 - [oasr use](USE.md) - **Deprecated**, use `oasr clone` instead (will be removed in v0.5.0)
 

oasr-0.4.2/docs/commands/CLEAN.md

@@ -0,0 +1,13 @@
+# `oasr clean` (DEPRECATED)
+
+> **⚠️ Warning: This command is deprecated and will be removed in v0.6.0.**  
+> Use `oasr registry prune` instead.
+
+Remove orphaned manifests and entries for missing skills.
+
+```bash
+oasr clean              # Shows deprecation warning
+oasr registry prune     # New command (recommended)
+```
+
+This command now delegates to `oasr registry prune`. See [REGISTRY.md](./REGISTRY.md#oasr-registry-prune) for full documentation.

{oasr-0.4.1 → oasr-0.4.2}/docs/commands/REGISTRY.md

@@ -105,6 +105,40 @@ Syncing remote skills...
 Synced: 2 skills
 ```
 
+### `oasr registry prune`
+
+Clean up corrupted/missing skills and orphaned artifacts:
+
+```bash
+oasr registry prune              # Interactive cleanup
+oasr registry prune -y           # Skip confirmation
+oasr registry prune --dry-run    # Show what would be cleaned
+oasr registry prune --json       # JSON output
+```
+
+This command:
+- Removes skills whose source files/URLs are no longer accessible
+- Removes orphaned manifest files not in the registry
+- Requires confirmation unless `-y` flag is used
+
+**Example output:**
+```bash
+$ oasr registry prune
+Checking 3 remote skill(s)...
+  ↓ python-analyzer (checking GitHub...)
+  ✓ python-analyzer (checked)
+
+The following will be cleaned:
+
+Skills with missing sources:
+  ✗ old-skill (/path/to/missing)
+
+Proceed with cleanup? [y/N] y
+Removed skill: old-skill
+
+Cleaned 1 skill(s), 0 manifest(s)
+```
+
 ## Migration from v0.2.0
 
 The v0.3.0 CLI taxonomy reorganizes commands under the `registry` subcommand:
@@ -117,3 +151,5 @@ The v0.3.0 CLI taxonomy reorganizes commands under the `registry` subcommand:
 | `oasr status` | `oasr registry -v` |
 | `oasr sync` (manifest validation) | `oasr registry` |
 | `oasr sync --update` (remote sync) | `oasr registry sync` |
+
+**v0.4.1 update:** `oasr clean` → `oasr registry prune`

{oasr-0.4.1 → oasr-0.4.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "oasr"
-version = "0.4.1"
+version = "0.4.2"
 description = "CLI for managing agent skills across IDE integrations"
 readme = "README.md"
 requires-python = ">=3.10"

{oasr-0.4.1 → oasr-0.4.2}/src/cli.py

@@ -13,7 +13,7 @@ from pathlib import Path
 from commands import adapter, clean, clone, config, diff, exec, find, registry, sync, update, use, validate
 from commands import help as help_cmd
 
-__version__ = "0.4.1"
+__version__ = "0.4.2"
 
 
 def main(argv: list[str] | None = None) -> int:

oasr-0.4.2/src/commands/clean.py

@@ -0,0 +1,30 @@
+"""`asr clean` command - DEPRECATED, use `oasr registry prune` instead."""
+
+from __future__ import annotations
+
+import argparse
+import sys
+
+
+def register(subparsers) -> None:
+    p = subparsers.add_parser(
+        "clean",
+        help="(Deprecated) Clean up corrupted/missing skills - use 'oasr registry prune'",
+    )
+    p.add_argument("-y", "--yes", action="store_true", help="Skip confirmation prompt")
+    p.add_argument("--json", action="store_true", help="Output in JSON format")
+    p.add_argument("--dry-run", action="store_true", help="Show what would be cleaned without doing it")
+    p.set_defaults(func=run)
+
+
+def run(args: argparse.Namespace) -> int:
+    """Delegate to registry prune with deprecation warning."""
+    # Show deprecation warning unless --json or --quiet
+    if not args.json:
+        print("⚠ Warning: 'oasr clean' is deprecated. Use 'oasr registry prune' instead.", file=sys.stderr)
+        print("   This command will be removed in v0.6.0.\n", file=sys.stderr)
+
+    # Delegate to registry prune
+    from commands.registry import run_prune
+
+    return run_prune(args)

{oasr-0.4.1 → oasr-0.4.2}/src/commands/registry.py

@@ -64,6 +64,13 @@ def register(subparsers) -> None:
     sync_p.add_argument("--config", type=Path, help="Override config file path")
     sync_p.set_defaults(func=run_sync)
 
+    # registry prune
+    prune_p = registry_subparsers.add_parser("prune", help="Clean up corrupted/missing skills and orphaned artifacts")
+    prune_p.add_argument("-y", "--yes", action="store_true", help="Skip confirmation prompt")
+    prune_p.add_argument("--json", action="store_true", help="Output in JSON format")
+    prune_p.add_argument("--dry-run", action="store_true", help="Show what would be cleaned without doing it")
+    prune_p.set_defaults(func=run_prune)
+
 
 def run_validate(args: argparse.Namespace) -> int:
     """Validate registry manifests (default oasr registry behavior)."""
@@ -301,3 +308,140 @@ def run_sync(args: argparse.Namespace) -> int:
             print(f"{len(pruned)} skill(s) pruned")
 
     return 1 if missing_count > 0 else 0
+
+
+def run_prune(args: argparse.Namespace) -> int:
+    """Clean up corrupted/missing skills and orphaned artifacts (oasr registry prune)."""
+    from manifest import delete_manifest, list_manifests
+
+    entries = load_registry()
+    registered_names = {e.name for e in entries}
+    manifest_names = set(list_manifests())
+
+    to_remove_skills = []
+    to_remove_manifests = []
+
+    # Check for remote skills and show progress header
+    remote_count = 0
+    for entry in entries:
+        manifest = load_manifest(entry.name)
+        if manifest and is_remote_source(manifest.source_path):
+            remote_count += 1
+
+    if remote_count > 0 and not args.json:
+        print(f"Checking {remote_count} remote skill(s)...", file=sys.stderr)
+
+    for entry in entries:
+        manifest = load_manifest(entry.name)
+        if manifest:
+            # Show progress for remote skills
+            is_remote = is_remote_source(manifest.source_path)
+            if is_remote and not args.json:
+                platform = (
+                    "GitHub"
+                    if "github.com" in manifest.source_path
+                    else "GitLab"
+                    if "gitlab.com" in manifest.source_path
+                    else "remote"
+                )
+                print(f"  ↓ {entry.name} (checking {platform}...)", file=sys.stderr, flush=True)
+
+            status = check_manifest(manifest)
+
+            if is_remote and not args.json:
+                print(f"  ✓ {entry.name} (checked)", file=sys.stderr)
+
+            if status.status == "missing":
+                to_remove_skills.append(
+                    {
+                        "name": entry.name,
+                        "reason": "source missing",
+                        "path": entry.path,
+                    }
+                )
+
+    orphaned = manifest_names - registered_names
+    for name in orphaned:
+        to_remove_manifests.append(
+            {
+                "name": name,
+                "reason": "orphaned manifest (not in registry)",
+            }
+        )
+
+    if not to_remove_skills and not to_remove_manifests:
+        if args.json:
+            print(json.dumps({"cleaned": 0, "message": "nothing to clean"}))
+        else:
+            print("Nothing to clean.")
+        return 0
+
+    if args.json:
+        result = {
+            "skills_to_remove": to_remove_skills,
+            "manifests_to_remove": to_remove_manifests,
+            "dry_run": args.dry_run,
+        }
+        if not args.dry_run and not args.yes:
+            result["requires_confirmation"] = True
+        print(json.dumps(result, indent=2))
+        if args.dry_run:
+            return 0
+    else:
+        print("The following will be cleaned:\n")
+
+        if to_remove_skills:
+            print("Skills with missing sources:")
+            for s in to_remove_skills:
+                print(f"  ✗ {s['name']} ({s['path']})")
+
+        if to_remove_manifests:
+            print("\nOrphaned manifests:")
+            for m in to_remove_manifests:
+                print(f"  ✗ {m['name']}")
+
+        print()
+
+        if args.dry_run:
+            print("(dry run - no changes made)")
+            return 0
+
+    if not args.yes and not args.json:
+        try:
+            response = input("Proceed with cleanup? [y/N] ").strip().lower()
+            if response not in ("y", "yes"):
+                print("Aborted.")
+                return 1
+        except (EOFError, KeyboardInterrupt):
+            print("\nAborted.")
+            return 1
+
+    removed_skills = []
+    removed_manifests = []
+
+    for s in to_remove_skills:
+        remove_skill(s["name"])
+        removed_skills.append(s["name"])
+
+    for m in to_remove_manifests:
+        delete_manifest(m["name"])
+        removed_manifests.append(m["name"])
+
+    if args.json:
+        print(
+            json.dumps(
+                {
+                    "removed_skills": removed_skills,
+                    "removed_manifests": removed_manifests,
+                },
+                indent=2,
+            )
+        )
+    else:
+        for name in removed_skills:
+            print(f"Removed skill: {name}")
+        for name in removed_manifests:
+            print(f"Removed manifest: {name}")
+        print(f"\nCleaned {len(removed_skills)} skill(s), {len(removed_manifests)} manifest(s)")
+
+    return 0

{oasr-0.4.1 → oasr-0.4.2}/uv.lock

@@ -138,7 +138,7 @@ wheels = [
 
 [[package]]
 name = "oasr"
-version = "0.4.0"
+version = "0.4.2"
 source = { editable = "." }
 dependencies = [
     { name = "pyyaml" },

oasr-0.4.1/docs/commands/CLEAN.md

@@ -1,11 +0,0 @@
-# `oasr clean`
-
-Remove orphaned manifests and entries for missing skills.
-
-```bash
-oasr clean
-oasr clean --dry-run
-```
-
-> **note**  
-> The same behaviour can be achieved using `oasr sync --prune`

oasr-0.4.1/doctor/SKILL.md

@@ -1,35 +0,0 @@
----
-name: doctor
-license: MIT
-description: 'Diagnoses software failures by combining deterministic evidence gathering
-  with agent judgment. Models failures as medical cases. Idempotent — run repeatedly
-  until confident diagnosis, then generate schema-based treatment.
-
-  '
-metadata:
-  author: Jordan Godau
-  version: 0.2.0
-  references:
-  - 00_ROUTER.md
-  - 01_SUMMARY.md
-  - 02_TRIGGERS.md
-  - 03_ALWAYS.md
-  - 04_NEVER.md
-  - 05_PROCEDURE.md
-  - 06_FAILURES.md
-  keywords:
-  - diagnose
-  - debug
-  - investigate
-  - evidence
-  - hypothesis
-  - treatment
-  oasr:
-    hash: sha256:f9fda45b7797923e9379e36c1b519c40b09f05f78bfa172a9d006c14b7283535
-    source: /home/jgodau/work/personal/skills/doctor/doctor
-    synced: '2026-02-01T06:35:54.685306Z'
----
-
-# INSTRUCTIONS
-
-1. Refer to `metadata.references`.

oasr-0.4.1/doctor/assets/schemas/session.schema.yaml

@@ -1,87 +0,0 @@
-# Doctor Session Schema
-# Artifact: .doctor/session.yaml
-
-type: object
-required:
-  - status
-  - created_at
-
-properties:
-  status:
-    type: string
-    enum: [investigating, diagnosed, treated, abandoned]
-    description: Current session status
-
-  created_at:
-    type: string
-    format: date-time
-    description: RFC3339 UTC timestamp
-
-  updated_at:
-    type: string
-    format: date-time
-    description: RFC3339 UTC timestamp of last update
-
-  patient:
-    type: string
-    description: Repository or system name
-
-  symptoms:
-    type: array
-    items:
-      type: object
-      properties:
-        description:
-          type: string
-        category:
-          type: string
-          enum: [error, timeout, crash, wrong_output, performance, unknown]
-        evidence:
-          type: string
-    description: Observed symptoms
-
-  hypotheses:
-    type: array
-    items:
-      type: object
-      properties:
-        description:
-          type: string
-        confidence:
-          type: integer
-          minimum: 0
-          maximum: 100
-        evidence_for:
-          type: array
-          items:
-            type: string
-        evidence_against:
-          type: array
-          items:
-            type: string
-        falsifiable_by:
-          type: string
-    description: Working hypotheses with confidence
-
-  diagnosis:
-    type: object
-    properties:
-      summary:
-        type: string
-      confidence:
-        type: integer
-        minimum: 0
-        maximum: 100
-      root_cause:
-        type: string
-      contributing_factors:
-        type: array
-        items:
-          type: string
-    description: Final diagnosis (when confident)
-
-  evidence_files:
-    type: array
-    items:
-      type: string
-    description: Paths to evidence snapshots in .doctor/evidence/

oasr-0.4.1/doctor/assets/schemas/treatment.schema.yaml

@@ -1,70 +0,0 @@
-# Treatment Plan Schema
-# Artifact: .doctor/treatment.md (generated from this schema)
-
-type: object
-required:
-  - diagnosis_summary
-  - confidence
-  - options
-
-properties:
-  diagnosis_summary:
-    type: string
-    description: One-line diagnosis
-
-  confidence:
-    type: integer
-    minimum: 0
-    maximum: 100
-    description: Diagnosis confidence percentage
-
-  root_cause:
-    type: string
-    description: Identified root cause
-
-  options:
-    type: array
-    minItems: 1
-    items:
-      type: object
-      required:
-        - name
-        - description
-        - risk
-      properties:
-        name:
-          type: string
-          description: Short option name
-        description:
-          type: string
-          description: What this option does
-        risk:
-          type: string
-          enum: [low, medium, high]
-        effort:
-          type: string
-          enum: [trivial, small, medium, large]
-        reversible:
-          type: boolean
-        steps:
-          type: array
-          items:
-            type: string
-          description: Ordered implementation steps
-    description: Treatment options (at least one required)
-
-  recommended:
-    type: string
-    description: Name of recommended option
-
-  caveats:
-    type: array
-    items:
-      type: string
-    description: Warnings or considerations
-
-  follow_up:
-    type: array
-    items:
-      type: string
-    description: Suggested follow-up actions

oasr-0.4.1/doctor/references/00_ROUTER.md

@@ -1,104 +0,0 @@
----
-description: Conditional dispatch for which reference files to load.
-index:
-  - Preconditions
-  - Routes
----
-
-# Router
-
----
-
-## Preconditions
-
-### Execute
-
-1. scripts/router_checks.sh --check session
-2. scripts/router_checks.sh --check treatment
-
-### Fresh Start Override
-
-If the user explicitly requests a fresh start, force the router into the `default` route by making the checks fail deterministically:
-
-1. Set `DOCTOR_FRESH_START=1` for the router check invocation, **or**
-2. Pass `--fresh-start` to `scripts/router_checks.sh`
-
-### Check
-
-- If user explicitly requests a fresh start, treat as `default` even if artifacts exist.
-
----
-
-## Routes
-
-1. treatment-complete
-2. session-active
-3. default
-
----
-
-### treatment-complete
-
-Resume after a treatment plan has already been generated.
-
-**When:**
-
-- `scripts/router_checks.sh --check treatment` exits 0
-
-**Read:**
-
-1. 01_SUMMARY.md
-
-**Ignore:**
-
-1. 02_TRIGGERS.md
-2. 03_ALWAYS.md
-3. 04_NEVER.md
-4. 05_PROCEDURE.md
-5. 06_FAILURES.md
-
----
-
-### session-active
-
-Resume mid-investigation when a session exists but treatment is not yet generated.
-
-**When:**
-
-- `scripts/router_checks.sh --check session` exits 0
-- `scripts/router_checks.sh --check treatment` exits non-zero
-
-**Read:**
-
-1. 01_SUMMARY.md
-2. 03_ALWAYS.md
-3. 05_PROCEDURE.md
-
-**Ignore:**
-
-1. 02_TRIGGERS.md
-2. 04_NEVER.md
-3. 06_FAILURES.md
-
----
-
-### default
-
-Fresh invocation — read all references in order.
-
-**When:**
-
-- No other route matches
-
-**Read:**
-
-1. 01_SUMMARY.md
-2. 02_TRIGGERS.md
-3. 03_ALWAYS.md
-4. 04_NEVER.md
-5. 05_PROCEDURE.md
-6. 06_FAILURES.md
-
-**Ignore:**
-
-(none)

oasr-0.4.1/doctor/references/01_SUMMARY.md

@@ -1,44 +0,0 @@
----
-description: What this skill is and is not.
-index:
-  - What It Does
-  - What Problems It Solves
-  - What It Is Not
-  - Key Invariant
-  - Artifact Location
----
-
-# Summary
-
-The **doctor** skill diagnoses software failures by combining deterministic evidence gathering with agent judgment.
-
-## What It Does
-
-- Models software failures as medical cases
-- Gathers evidence through parameterized search (agent provides terms, script returns matches)
-- Tracks symptoms, hypotheses, and confidence levels
-- Produces schema-based treatment plans when diagnosis is confident
-
-## What Problems It Solves
-
-- Prevents premature action on incomplete understanding
-- Separates observation from interpretation
-- Makes uncertainty explicit (confidence percentages)
-- Creates reviewable artifacts for handoff
-
-## What It Is Not
-
-- Not a fix-it skill (produces plans, not changes)
-- Not a sequential pipeline (idempotent, run until confident)
-- Not purely deterministic (balances scripts with agent reasoning)
-
-## Key Invariant
-
-**Execution means investigation, not implementation.** The skill gathers evidence and produces treatment plans. It does not execute fixes.
-
-## Artifact Location
-
-All artifacts stored in `.doctor/`:
-- `session.yaml` — Current diagnosis state
-- `evidence/` — Evidence snapshots
-- `treatment.md` — Generated treatment plan