# File Safety

> File modification rules to prevent overwriting important files. Use when overwriting existing files, deleting files, or writing to directories that contain important data (data/, outs/). Also applies when moving or renaming files that other scripts depend on.

- Skill: `majiayu000/file-safety` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add majiayu000/file-safety`
- Raw SKILL.md: https://api.skillmd.com/api/skills/majiayu000/file-safety/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: majiayu000 (https://skillmd.com/u/majiayu000)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/majiayu000/file-safety

---


# File Modification Rules (CRITICAL)

## General Rules (All Projects)

### Never Overwrite These Files

1. **Outputs from someone else** — files from collaborators, students, or external sources
2. **Original/source data** — anything you did not generate in this session
3. **Configuration files** — unless the user explicitly requests changes

### Instead

- Create a **new file with an updated name** (e.g., add `_updated`, `_with_new_column`)
- **Ask the user** before modifying if uncertain about the file's origin

### Files You CAN Overwrite

- Files you created in the current session
- Configuration files when the user requests changes

### Script Output Integrity

**Never create standalone scripts solely to modify outputs from other scripts.**

If modifications are needed:

1. **Modify the original script** — if the change belongs upstream, update the source (ask user first)
2. **Handle in downstream scripts** — do the transformation as part of the consuming script's workflow

**Do NOT** create intermediate "fixer" scripts that modify upstream outputs after the fact — this breaks the reproducibility chain between scripts and their outputs.

### When Uncertain

If you're not sure whether a file is safe to overwrite, ask:
- "This file exists — was it generated by another script or provided externally?"
- "Should I create a new file with a modified name, or is it safe to overwrite?"

---

## Data Science Projects (with data/ and outs/ directories)

These additional rules apply in projects with `project-type: data-science` or that use the `script-organization` conventions (numbered scripts, `data/` for inputs, `outs/` for outputs).

### Output Ownership

Each script writes **only** to its own output folder under `outs/`. Never write to another script's output folder.

```r
# Script 03_plots.qmd writes ONLY to:
out_dir <- here("outs/03_plots")

# NEVER write to another script's folder:
# here("outs/01_analysis/modified_data.rds")  # WRONG
```

### `data/` is Read-Only

Scripts never write to `data/`. This directory contains only external/immutable inputs (raw data, collaborator files, annotations). If your code produced it, it goes in `outs/`.

### Example

```r
# BAD: Creating a script to add Gene.short to another script's output
# This disconnects the file from the script that produced it

# GOOD: Downstream plotting script joins against lookup at runtime
limma_res <- readRDS(here("outs/01_analysis/limma_results_annotated.rds")) %>%
  left_join(gene_name_lookup, by = "trinity_gene_id")
```