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fix(init): prevent clobbering instruction files (GEMINI.md, RTK.md) #835

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fix(init): prevent clobbering instruction files (GEMINI.md, RTK.md) #835

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180 changes: 158 additions & 22 deletions src/hooks/init.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -588,12 +588,10 @@ pub fn uninstall(global: bool, gemini: bool, codex: bool, cursor: bool, verbose:
removed.push("Integrity hash: removed".to_string());
}

// 2. Remove RTK.md
// 2. Remove RTK.md RTK block
let rtk_md_path = claude_dir.join("RTK.md");
if rtk_md_path.exists() {
fs::remove_file(&rtk_md_path)
.with_context(|| format!("Failed to remove RTK.md: {}", rtk_md_path.display()))?;
removed.push(format!("RTK.md: {}", rtk_md_path.display()));
if remove_rtk_block_from_file(&rtk_md_path, "RTK.md", verbose)? {
removed.push("RTK.md: removed RTK block".to_string());
}

// 3. Remove @RTK.md reference from CLAUDE.md
Expand Down Expand Up @@ -674,13 +672,8 @@ fn uninstall_codex_at(codex_dir: &Path, verbose: u8) -> Result<Vec<String>> {
let mut removed = Vec::new();

let rtk_md_path = codex_dir.join("RTK.md");
if rtk_md_path.exists() {
fs::remove_file(&rtk_md_path)
.with_context(|| format!("Failed to remove RTK.md: {}", rtk_md_path.display()))?;
if verbose > 0 {
eprintln!("Removed RTK.md: {}", rtk_md_path.display());
}
removed.push(format!("RTK.md: {}", rtk_md_path.display()));
if remove_rtk_block_from_file(&rtk_md_path, "RTK.md", verbose)? {
removed.push("RTK.md: removed RTK block".to_string());
}

let agents_md_path = codex_dir.join("AGENTS.md");
Expand Down Expand Up @@ -905,8 +898,8 @@ fn run_default_mode(
let (_hook_dir, hook_path) = prepare_hook_paths()?;
let hook_changed = ensure_hook_installed(&hook_path, verbose)?;

// 2. Write RTK.md
write_if_changed(&rtk_md_path, RTK_SLIM, "RTK.md", verbose)?;
// 2. Write RTK.md (use upsert to avoid clobbering user content)
upsert_write_rtk_block(&rtk_md_path, RTK_SLIM, "RTK.md", verbose)?;

let opencode_plugin_path = if install_opencode {
let path = prepare_opencode_plugin_path()?;
Expand Down Expand Up @@ -1264,7 +1257,8 @@ fn run_codex_mode(global: bool, verbose: u8) -> Result<()> {
}
}

write_if_changed(&rtk_md_path, RTK_SLIM_CODEX, "RTK.md", verbose)?;
// Use upsert to avoid clobbering user content
upsert_write_rtk_block(&rtk_md_path, RTK_SLIM_CODEX, "RTK.md", verbose)?;
let added_ref = patch_agents_md(&agents_md_path, verbose)?;

println!("\nRTK configured for Codex CLI.\n");
Expand Down Expand Up @@ -1352,6 +1346,85 @@ fn upsert_rtk_block(content: &str, block: &str) -> (String, RtkBlockUpsert) {
}
}

/// Upsert-based file write for instructions (RTK.md, GEMINI.md, etc.)
/// Wraps content in markers and appends if not present, or updates the existing block
fn upsert_write_rtk_block(path: &Path, content: &str, name: &str, verbose: u8) -> Result<bool> {
let block = format!(
"<!-- rtk-instructions v2 -->\n{}\n<!-- /rtk-instructions -->",
content.trim()
);

let existing = if path.exists() {
fs::read_to_string(path)
.with_context(|| format!("Failed to read {}: {}", name, path.display()))?
} else {
String::new()
};

let (new_content, action) = upsert_rtk_block(&existing, &block);

match action {
RtkBlockUpsert::Unchanged => {
if verbose > 0 {
eprintln!("{} already up to date: {}", name, path.display());
}
Ok(false)
}
RtkBlockUpsert::Added | RtkBlockUpsert::Updated => {
atomic_write(path, &new_content)
.with_context(|| format!("Failed to write {}: {}", name, path.display()))?;
if verbose > 0 {
if action == RtkBlockUpsert::Added {
eprintln!("Created/Appended {}: {}", name, path.display());
} else {
eprintln!("Updated {}: {}", name, path.display());
}
}
Ok(true)
}
RtkBlockUpsert::Malformed => {
eprintln!(
"[warn] Warning: Found incomplete rtk-instructions block in {}",
path.display()
);
Ok(false)
}
}
}

/// Remove RTK instructions block from a file (RTK.md, GEMINI.md, etc.)
/// Deletes the file if it becomes empty after removing the block
fn remove_rtk_block_from_file(path: &Path, name: &str, verbose: u8) -> Result<bool> {
if !path.exists() {
return Ok(false);
}

let existing = fs::read_to_string(path)
.with_context(|| format!("Failed to read {}: {}", name, path.display()))?;

let (new_content, did_remove) = remove_rtk_block(&existing);

if did_remove {
let trimmed = new_content.trim();
if trimmed.is_empty() {
fs::remove_file(path)
.with_context(|| format!("Failed to remove empty {}: {}", name, path.display()))?;
if verbose > 0 {
eprintln!("Removed empty {}: {}", name, path.display());
}
} else {
atomic_write(path, &new_content)
.with_context(|| format!("Failed to update {}: {}", name, path.display()))?;
if verbose > 0 {
eprintln!("Removed RTK block from {}: {}", name, path.display());
}
}
Ok(true)
} else {
Ok(false)
}
}

/// Patch CLAUDE.md: add @RTK.md, migrate if old block exists
fn patch_claude_md(path: &Path, verbose: u8) -> Result<bool> {
let mut content = if path.exists() {
Expand Down Expand Up @@ -2147,8 +2220,8 @@ pub fn run_gemini(global: bool, hook_only: bool, patch_mode: PatchMode, verbose:
// 2. Install GEMINI.md (RTK awareness for Gemini)
if !hook_only {
let gemini_md_path = gemini_dir.join("GEMINI.md");
// Reuse the same slim RTK awareness content
write_if_changed(&gemini_md_path, RTK_SLIM, "GEMINI.md", verbose)?;
// Use upsert to avoid clobbering existing user content in GEMINI.md
upsert_write_rtk_block(&gemini_md_path, RTK_SLIM, "GEMINI.md", verbose)?;
}

// 3. Patch ~/.gemini/settings.json
Expand Down Expand Up @@ -2276,12 +2349,10 @@ fn uninstall_gemini(verbose: u8) -> Result<Vec<String>> {
removed.push(format!("Gemini hook: {}", hook_path.display()));
}

// Remove GEMINI.md
// Remove GEMINI.md RTK block
let gemini_md = gemini_dir.join("GEMINI.md");
if gemini_md.exists() {
fs::remove_file(&gemini_md)
.with_context(|| format!("Failed to remove {}", gemini_md.display()))?;
removed.push(format!("GEMINI.md: {}", gemini_md.display()));
if remove_rtk_block_from_file(&gemini_md, "GEMINI.md", verbose)? {
removed.push(format!("GEMINI.md: removed RTK block"));
}

// Remove hook from settings.json
Expand Down Expand Up @@ -2584,6 +2655,71 @@ More notes
assert_eq!(content, input);
}

#[test]
fn test_upsert_write_rtk_block() {
let temp = TempDir::new().unwrap();
let path = temp.path().join("GEMINI.md");
let name = "GEMINI.md";
let content = "Test content";

// 1. Create new
let changed = upsert_write_rtk_block(&path, content, name, 0).unwrap();
assert!(changed);
let result = fs::read_to_string(&path).unwrap();
assert!(result.contains("<!-- rtk-instructions v2 -->"));
assert!(result.contains("Test content"));
assert!(result.contains("<!-- /rtk-instructions -->"));

// 2. Update existing (no-op)
let changed = upsert_write_rtk_block(&path, content, name, 0).unwrap();
assert!(!changed);

// 3. Update existing (content change)
let changed = upsert_write_rtk_block(&path, "New content", name, 0).unwrap();
assert!(changed);
let result = fs::read_to_string(&path).unwrap();
assert!(result.contains("New content"));
assert!(!result.contains("Test content"));

// 4. Preserve surrounding content
fs::write(&path, format!("Header\n\n{result}\n\nFooter")).unwrap();
let changed = upsert_write_rtk_block(&path, "Updated block", name, 0).unwrap();
assert!(changed);
let result = fs::read_to_string(&path).unwrap();
assert!(result.starts_with("Header"));
assert!(result.contains("Updated block"));
assert!(result.ends_with("Footer"));
}

#[test]
fn test_remove_rtk_block_from_file() {
let temp = TempDir::new().unwrap();
let path = temp.path().join("GEMINI.md");
let name = "GEMINI.md";

// 1. Remove from missing file
let removed = remove_rtk_block_from_file(&path, name, 0).unwrap();
assert!(!removed);

// 2. Remove block leaving file empty (should delete file)
let block = "<!-- rtk-instructions v2 -->\ncontent\n<!-- /rtk-instructions -->";
fs::write(&path, block).unwrap();
let removed = remove_rtk_block_from_file(&path, name, 0).unwrap();
assert!(removed);
assert!(!path.exists());

// 3. Remove block preserving other content
let content = format!("Header\n\n{block}\n\nFooter");
fs::write(&path, content).unwrap();
let removed = remove_rtk_block_from_file(&path, name, 0).unwrap();
assert!(removed);
assert!(path.exists());
let result = fs::read_to_string(&path).unwrap();
assert!(result.contains("Header"));
assert!(result.contains("Footer"));
assert!(!result.contains("rtk-instructions"));
}

#[test]
fn test_init_is_idempotent() {
let temp = TempDir::new().unwrap();
Expand Down