feat(index): add --hidden flag for dot-prefixed files

CHANGELOG.md

@@ -5,6 +5,7 @@ All notable changes to this project will be documented in this file.
 ## [Unreleased]
 
 ### Added
+- **`--hidden` flag**: Include hidden (dot-prefixed) files and directories in indexing and search operations
 - **VitePress documentation site**: Comprehensive documentation with improved navigation, search, and structure in `docs-site/` directory
 - **Documentation features**: Guide pages, feature documentation, CLI reference, embedding model guide, architecture docs, and contributing guides
 - **Local search**: Built-in search functionality in documentation site

ck-cli/src/main.rs

@@ -247,6 +247,9 @@ struct Cli {
     #[arg(long = "no-ckignore", help = "Don't respect .ckignore file")]
     no_ckignore: bool,
 
+    #[arg(long = "hidden", help = "Include hidden (dot-prefixed) files and directories")]
+    hidden: bool,
+
     #[arg(
         long = "print-default-ckignore",
         help = "Print the default .ckignore content that ck generates and exit"
@@ -631,6 +634,7 @@ async fn run_index_workflow(
         respect_gitignore: !cli.no_ignore,
         use_ckignore: !cli.no_ckignore,
         exclude_patterns: exclude_patterns.clone(),
+        show_hidden: cli.hidden,
     };
     let index_future = ck_index::smart_update_index_with_detailed_progress(
         path,
@@ -1078,6 +1082,7 @@ async fn run_cli_mode(cli: Cli) -> Result<()> {
                 respect_gitignore: !cli.no_ignore,
                 use_ckignore: !cli.no_ckignore,
                 exclude_patterns: exclude_patterns.clone(),
+                show_hidden: cli.hidden,
             };
             let cleanup_stats = ck_index::cleanup_index(&clean_path, &file_options)?;
             status.finish_progress(cleanup_spinner, "Cleanup complete");
@@ -1466,6 +1471,7 @@ fn build_options(cli: &Cli, reindex: bool, _repo_root: Option<&Path>) -> SearchO
         respect_gitignore: !cli.no_ignore,
         use_ckignore: !cli.no_ckignore,
         full_section: cli.full_section,
+        hidden: cli.hidden,
         // Enhanced embedding options (search-time only)
         rerank: cli.rerank,
         rerank_model: cli.rerank_model.clone(),

ck-cli/src/mcp/context.rs

@@ -55,6 +55,7 @@ impl McpContext {
             respect_gitignore: true,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: false,
             rerank_model: None,
             embedding_model: None,

ck-cli/src/mcp/session.rs

@@ -465,6 +465,7 @@ mod tests {
             respect_gitignore: true,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: false,
             rerank_model: None,
             embedding_model: None,

ck-cli/src/mcp_server.rs

@@ -1088,6 +1088,7 @@ impl CkMcpServer {
             respect_gitignore,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: request.rerank.unwrap_or(false),
             rerank_model: request.rerank_model.clone(),
             embedding_model: None,
@@ -1295,6 +1296,7 @@ impl CkMcpServer {
             respect_gitignore,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: false,
             rerank_model: None,
             embedding_model: None,
@@ -1430,6 +1432,7 @@ impl CkMcpServer {
             respect_gitignore,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: false,
             rerank_model: None,
             embedding_model: None,
@@ -1565,6 +1568,7 @@ impl CkMcpServer {
             respect_gitignore,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: request.rerank.unwrap_or(false),
             rerank_model: request.rerank_model.clone(),
             embedding_model: None,
@@ -1820,6 +1824,7 @@ impl CkMcpServer {
             respect_gitignore: true,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: false,
             rerank_model: None,
             embedding_model: None,

ck-cli/tests/integration_tests.rs

@@ -821,3 +821,81 @@ fn test_add_file_with_relative_path() {
     let stdout = String::from_utf8(output.stdout).unwrap();
     assert!(stdout.contains("Relative path content"));
 }
+
+#[test]
+#[serial]
+fn test_hidden_flag_includes_hidden_files() {
+    let temp_dir = TempDir::new().unwrap();
+
+    // Create a regular file
+    fs::write(temp_dir.path().join("visible.txt"), "visible content").unwrap();
+
+    // Create a hidden directory with a file inside
+    let hidden_dir = temp_dir.path().join(".hidden-test");
+    fs::create_dir(&hidden_dir).unwrap();
+    fs::write(hidden_dir.join("secret.txt"), "hidden secret content").unwrap();
+
+    // Create a hidden file at root level
+    fs::write(temp_dir.path().join(".hidden-file.txt"), "hidden file content").unwrap();
+
+    // First, index WITHOUT --hidden flag
+    let output = Command::new(ck_binary())
+        .args(["--index", "."])
+        .current_dir(temp_dir.path())
+        .output()
+        .expect("Failed to run ck --index");
+
+    assert!(output.status.success());
+
+    // Search for "hidden" - should NOT find the hidden files
+    let output = Command::new(ck_binary())
+        .args(["hidden", "."])
+        .current_dir(temp_dir.path())
+        .output()
+        .expect("Failed to run ck search");
+
+    let stdout = String::from_utf8(output.stdout).unwrap();
+    // Should not contain hidden directory content
+    assert!(
+        !stdout.contains("hidden secret content"),
+        "Hidden directory content should NOT be indexed without --hidden flag"
+    );
+    assert!(
+        !stdout.contains("hidden file content"),
+        "Hidden file content should NOT be indexed without --hidden flag"
+    );
+
+    // Clean the index
+    let _ = Command::new(ck_binary())
+        .args(["--clean", "."])
+        .current_dir(temp_dir.path())
+        .output()
+        .expect("Failed to run ck --clean");
+
+    // Now index WITH --hidden flag
+    let output = Command::new(ck_binary())
+        .args(["--hidden", "--index", "."])
+        .current_dir(temp_dir.path())
+        .output()
+        .expect("Failed to run ck --hidden --index");
+
+    assert!(output.status.success());
+
+    // Search for "hidden" WITH --hidden flag - should now find the hidden files
+    let output = Command::new(ck_binary())
+        .args(["--hidden", "hidden", "."])
+        .current_dir(temp_dir.path())
+        .output()
+        .expect("Failed to run ck search");
+
+    let stdout = String::from_utf8(output.stdout).unwrap();
+    // Should now contain hidden directory content
+    assert!(
+        stdout.contains("hidden secret content"),
+        "Hidden directory content should be indexed with --hidden flag"
+    );
+    assert!(
+        stdout.contains("hidden file content"),
+        "Hidden file content should be indexed with --hidden flag"
+    );
+}

ck-core/src/lib.rs

@@ -298,6 +298,19 @@ pub struct FileCollectionOptions {
     pub use_ckignore: bool,
     /// Patterns to exclude files/directories
     pub exclude_patterns: Vec<String>,
+    /// Whether to include hidden (dot-prefixed) files and directories
+    pub show_hidden: bool,
+}
+
+impl Default for FileCollectionOptions {
+    fn default() -> Self {
+        Self {
+            respect_gitignore: true,
+            use_ckignore: true,
+            exclude_patterns: Vec::new(),
+            show_hidden: false,
+        }
+    }
 }
 
 impl From<&SearchOptions> for FileCollectionOptions {
@@ -306,6 +319,7 @@ impl From<&SearchOptions> for FileCollectionOptions {
             respect_gitignore: opts.respect_gitignore,
             use_ckignore: true, // Always use .ckignore for hierarchical ignore support
             exclude_patterns: opts.exclude_patterns.clone(),
+            show_hidden: opts.hidden,
         }
     }
 }
@@ -338,6 +352,7 @@ pub struct SearchOptions {
     pub respect_gitignore: bool,
     pub use_ckignore: bool,
     pub full_section: bool,
+    pub hidden: bool,
     // Enhanced embedding options (search-time only)
     pub rerank: bool,
     pub rerank_model: Option<String>,
@@ -395,6 +410,7 @@ impl Default for SearchOptions {
             respect_gitignore: true,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             // Enhanced embedding options (search-time only)
             rerank: false,
             rerank_model: None,

ck-engine/src/lib.rs

@@ -432,6 +432,7 @@ fn regex_search(options: &SearchOptions) -> Result<Vec<SearchResult>> {
             respect_gitignore: options.respect_gitignore,
             use_ckignore: true,
             exclude_patterns: options.exclude_patterns.clone(),
+            show_hidden: options.hidden,
         };
         let collected = ck_index::collect_files(&options.path, &file_options)?;
         filter_files_by_include(collected, &options.include_patterns)

ck-index/src/lib.rs

@@ -191,7 +191,7 @@ pub fn collect_files(
             .git_ignore(true)
             .git_global(true)
             .git_exclude(true)
-            .hidden(true);
+            .hidden(!options.show_hidden);
 
         // Add .ckignore support (hierarchical, like .gitignore)
         if options.use_ckignore {
@@ -213,7 +213,7 @@ pub fn collect_files(
         let combined_overrides = build_overrides(path, &all_patterns)?;
 
         let mut walker_builder = WalkBuilder::new(path);
-        walker_builder.git_ignore(false).hidden(true);
+        walker_builder.git_ignore(false).hidden(!options.show_hidden);
 
         // Add .ckignore support even without gitignore
         if options.use_ckignore {
@@ -1830,6 +1830,7 @@ mod tests {
             respect_gitignore: true,
             use_ckignore: true,
             exclude_patterns: vec![],
+            show_hidden: false,
         };
 
         // First index
@@ -1892,6 +1893,7 @@ mod tests {
             respect_gitignore: true,
             use_ckignore: true,
             exclude_patterns: vec![],
+            show_hidden: false,
         };
         let stats = cleanup_index(test_path, &file_options).unwrap();
         assert_eq!(stats.orphaned_entries_removed, 1);

ck-tui/src/app.rs

@@ -577,6 +577,7 @@ impl TuiApp {
             respect_gitignore: true,
             use_ckignore: true,
             full_section: false,
+            hidden: false,
             rerank: false,
             rerank_model: None,
             embedding_model: None,