update the repo

AGENT_SKILL/file_naming_convention/CHECKLIST.md

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+# Checklist: file_naming_convention
+
+## File/Directory Creation/Rename/Move
+- [ ] All new files and directories use `snake_case` (lowercase, digits, underscores only)
+- [ ] No spaces or special characters in file/directory names
+- [ ] Hyphens (`-`) used only in `docker-compose.yaml`, `docker-compose.yml`, `package-lock.json`, `yarn.lock`, `pnpm-lock.yaml`
+- [ ] `UPPER_SNAKE_CASE` used only for root-level configuration constants (e.g., `CONFIG.json`, `Dockerfile`)
+- [ ] Forbidden extensions (`.pdf`, `.pptx`, `.docx`, `.xlsx`, `.csv`, `.zip`, `.pth`, `.png`, `.jpg`, `.jpeg`, `.gif`, `.bmp`, `.tiff`, `.webp`, `.mp4`, `.mov`, `.avi`, `.dcm`, `.nii`, `.nii.gz`) are not present in the repository
+- [ ] Any file under `LEGACY/` that is modified includes an inline comment `# LEGACY:` explaining the change
+- [ ] Test files follow the pattern: `tests/<same_path_as_source>/test_<source_filename>`
+
+## Verification Steps
+1. Check all created/renamed/moved files for snake_case naming
+2. Verify hyphen usage is limited to allowed files: docker-compose.yaml/.yml, package-lock.json, yarn.lock, pnpm-lock.yaml
+3. Confirm UPPER_SNAKE_CASE appears only for root config files
+4. Scan for forbidden file extensions
+5. Inspect any changes in LEGACY/ directory for required comment
+6. Validate test file placement matches source file structure

AGENT_SKILL/file_naming_convention/EXAMPLES.md

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+# Examples: file_naming_convention
+
+## Correct Examples
+
+### File Naming
+- `patient_data.csv` → ❌ (forbidden extension, should be external)
+- `patient_data.json` → ✅ (allowed extension, snake_case)
+- `Dockerfile` → ✅ (UPPER_SNAKE_CASE allowed for root config)
+- `docker-compose.yaml` → ✅ (hyphen allowed exception)
+- `docker-compose.yml` → ✅ (hyphen allowed exception)
+- `package-lock.json` → ✅ (hyphen allowed exception)
+- `yarn.lock` → ✅ (hyphen allowed exception)
+- `pnpm-lock.yaml` → ✅ (hyphen allowed exception)
+- `config.json` → ✅ (snake_case, allowed extension)
+- `api/v1/patient_routes.py` → ✅ (snake_case in path)
+
+### Directory Naming
+- `data_models/` → ✅
+- `api_v2/` → ✅
+- `legacy_data/` → ✅ (but see LEGACY/ rule below)
+
+### LEGACY/ Directory
+```python
+# LEGACY: Temporary fix for migration issue #123
+# TODO: Remove after migration complete
+legacy_code_here()
+```
+→ ✅ (includes required comment)
+
+### Test Files
+```
+src/
+  models/
+    patient_model.py
+tests/
+  models/
+    test_patient_model.py
+```
+→ ✅ (test file mirrors source path)
+
+## Incorrect Examples
+
+### File Naming
+- `PatientData.json` → ❌ (PascalCase, should be snake_case)
+- `patient-data.json` → ❌ (hyphen not allowed except docker-compose and lockfiles)
+- `patient data.json` → ❌ (spaces not allowed)
+- `patient.PDF` → ❌ (forbidden extension)
+- `secret_key.pem` → ❌ (forbidden extension)
+- `package_lock.json` → ❌ (should be package-lock.json with hyphens)
+- `yarn_lock` → ❌ (should be yarn.lock with hyphen and extension)
+- `docker_compose.yaml` → ❌ (should be docker-compose.yaml with hyphens)
+
+### Directory Naming
+- `DataModels/` → ❌ (PascalCase)
+- `data-models/` → ❌ (hyphens not allowed)
+- `data models/` → ❌ (spaces)
+
+### LEGACY/ Directory
+```python
+# Modified legacy function
+def old_function():
+    pass
+```
+→ ❌ (missing `# LEGACY:` comment)
+
+### Test Files
+```
+src/
+  utils/
+    helper.py
+tests/
+  test_helper.py  # ❌ Incorrect: should be tests/utils/test_helper.py
+```
+→ ❌ (test file does not mirror source path)

AGENT_SKILL/file_naming_convention/SKILL.md

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+# Skill: file_naming_convention
+
+## Trigger Conditions
+Any file or directory create, rename, or move operation.
+
+## Rules
+
+### 1. File and Directory Naming
+- All files and directories must use `snake_case` (lowercase letters, digits, underscores only).
+- No spaces or special characters (except hyphens in specific cases).
+- Severity: `[ERROR]`
+
+### 2. Hyphen Usage Exception
+- Hyphens (`-`) are allowed ONLY in the following specific filenames (where changing the name would break standard tooling):
+  - `docker-compose.yaml`, `docker-compose.yml`
+  - `package-lock.json`, `yarn.lock`, `pnpm-lock.yaml`
+- Files beginning with '.' (like `.gitignore`, `.env`, `.npmrc`) are exempt from snake_case requirements for the prefix portion, but the suffix should follow naming conventions where practical.
+- Any other use of hyphens in file or directory names is prohibited.
+- Severity: `[ERROR]`
+
+### 3. Uppercase Reserved for Root Constants
+- `UPPER_SNAKE_CASE` is reserved only for root-level configuration constants (e.g., `CONFIG.json`, `Dockerfile`).
+- Using `UPPER_SNAKE_CASE` for regular files or directories is prohibited.
+- Severity: `[ERROR]`
+
+### 4. Forbidden Extensions
+The following file extensions are forbidden in the repository (must be stored externally and referenced by URL):
+- `.pdf`, `.pptx`, `.docx`, `.xlsx`, `.csv`, `.zip`, `.pth`, `.png`, `.jpg`, `.jpeg`, `.gif`, `.bmp`, `.tiff`, `.webp`, `.mp4`, `.mov`, `.avi`, `.dcm`, `.nii`, `.nii.gz`
+- Severity: `[ERROR]`
+
+### 5. LEGACY/ Directory Policy
+- The `LEGACY/` directory is read-only.
+- Any modification to files under `LEGACY/` must include an inline comment `# LEGACY:` explaining why the change is necessary.
+- Failure to include this comment when modifying LEGACY/ files is a violation.
+- Severity: `[ERROR]`
+
+### 6. Test File Naming
+- Test files must mirror the source file path in a parallel `tests/` directory.
+- Example: `src/module.py` → `tests/test_module.py`
+- Severity: `[WARN]`