fix: prevent hidden directories from being indexed

- Changed .hidden(false) to .hidden(true) in WalkBuilder configuration
- Fixes critical bug where .git and other hidden directories were indexed
- Eliminates .git files appearing in semantic search results
- Reduces index size and improves performance

The bug was causing:
- .git directory contents to be indexed as .ck/.git/...
- Semantic search finding git refs for unrelated queries
- Unnecessary storage and processing of hidden files

🤖 Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>

Author: runonthespot

CHANGELOG.md

@@ -2,6 +2,18 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.4.2] - 2025-09-11
+
+### Fixed
+- **Hidden file indexing bug**: Fixed critical bug where hidden directories (especially `.git`) were being indexed despite exclusion patterns
+- **Semantic search pollution**: Eliminated `.git` files appearing in semantic search results for unrelated queries
+- **Index size reduction**: Significantly reduced index size by properly excluding hidden files and directories
+
+### Technical
+- **WalkBuilder configuration**: Changed `.hidden(false)` to `.hidden(true)` to respect hidden file conventions
+- **Exclusion pattern enforcement**: Hidden file exclusion now takes precedence, preventing override patterns from being ignored
+- **Performance improvement**: Reduced indexing time and storage by not processing `.git` and other hidden directories
+
 ## [0.4.1] - 2025-09-10
 
 ### Added

Cargo.lock

@@ -12,7 +12,7 @@ members = [
 ]
 
 [workspace.package]
-version = "0.4.1"
+version = "0.4.2"
 edition = "2024"
 authors = ["Mike Renwick"]
 license = "MIT OR Apache-2.0"

Cargo.toml

@@ -11,7 +11,7 @@ keywords = ["search", "ann", "vector"]
 categories = ["algorithms"]
 
 [dependencies]
-ck-core = { version = "0.4.1", path = "../ck-core" }
+ck-core = { version = "0.4.2", path = "../ck-core" }
 
 anyhow = { workspace = true }
 serde = { workspace = true }

ck-ann/Cargo.toml

@@ -11,7 +11,7 @@ keywords = ["parsing", "chunking", "tree-sitter"]
 categories = ["parsing"]
 
 [dependencies]
-ck-core = { version = "0.4.1", path = "../ck-core" }
+ck-core = { version = "0.4.2", path = "../ck-core" }
 
 anyhow = { workspace = true }
 serde = { workspace = true }

ck-chunk/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ck-search"
-version = "0.4.1"
+version = "0.4.2"
 edition = "2024"
 authors = ["Mike Renwick"]
 license = "MIT OR Apache-2.0"
@@ -17,13 +17,13 @@ name = "ck"
 path = "src/main.rs"
 
 [dependencies]
-ck-core = { version = "0.4.1", path = "../ck-core" }
-ck-index = { version = "0.4.1", path = "../ck-index" }
-ck-engine = { version = "0.4.1", path = "../ck-engine" }
-ck-chunk = { version = "0.4.1", path = "../ck-chunk" }
-ck-embed = { version = "0.4.1", path = "../ck-embed" }
-ck-ann = { version = "0.4.1", path = "../ck-ann" }
-ck-models = { version = "0.4.1", path = "../ck-models" }
+ck-core = { version = "0.4.2", path = "../ck-core" }
+ck-index = { version = "0.4.2", path = "../ck-index" }
+ck-engine = { version = "0.4.2", path = "../ck-engine" }
+ck-chunk = { version = "0.4.2", path = "../ck-chunk" }
+ck-embed = { version = "0.4.2", path = "../ck-embed" }
+ck-ann = { version = "0.4.2", path = "../ck-ann" }
+ck-models = { version = "0.4.2", path = "../ck-models" }
 
 anyhow = { workspace = true }
 clap = { workspace = true }

ck-cli/Cargo.toml

@@ -11,7 +11,7 @@ keywords = ["embedding", "nlp", "semantic"]
 categories = ["science"]
 
 [dependencies]
-ck-core = { version = "0.4.1", path = "../ck-core" }
+ck-core = { version = "0.4.2", path = "../ck-core" }
 
 anyhow = { workspace = true }
 serde = { workspace = true }

ck-embed/Cargo.toml

@@ -11,11 +11,11 @@ keywords = ["search", "engine", "semantic"]
 categories = ["algorithms"]
 
 [dependencies]
-ck-core = { version = "0.4.1", path = "../ck-core" }
-ck-index = { version = "0.4.1", path = "../ck-index" }
-ck-embed = { version = "0.4.1", path = "../ck-embed" }
-ck-ann = { version = "0.4.1", path = "../ck-ann" }
-ck-chunk = { version = "0.4.1", path = "../ck-chunk" }
+ck-core = { version = "0.4.2", path = "../ck-core" }
+ck-index = { version = "0.4.2", path = "../ck-index" }
+ck-embed = { version = "0.4.2", path = "../ck-embed" }
+ck-ann = { version = "0.4.2", path = "../ck-ann" }
+ck-chunk = { version = "0.4.2", path = "../ck-chunk" }
 serde_json = { workspace = true }
 
 anyhow = { workspace = true }

ck-engine/Cargo.toml

@@ -11,9 +11,9 @@ keywords = ["indexing", "search", "storage"]
 categories = ["database-implementations"]
 
 [dependencies]
-ck-core = { version = "0.4.1", path = "../ck-core" }
-ck-chunk = { version = "0.4.1", path = "../ck-chunk" }
-ck-embed = { version = "0.4.1", path = "../ck-embed" }
+ck-core = { version = "0.4.2", path = "../ck-core" }
+ck-chunk = { version = "0.4.2", path = "../ck-chunk" }
+ck-embed = { version = "0.4.2", path = "../ck-embed" }
 
 anyhow = { workspace = true }
 serde = { workspace = true }

ck-index/Cargo.toml

@@ -88,7 +88,7 @@ pub fn collect_files(
             .git_ignore(true)
             .git_global(true)
             .git_exclude(true)
-            .hidden(false)
+            .hidden(true)
             .overrides(overrides)
             .build()
             .filter_map(|entry| entry.ok())
@@ -112,7 +112,7 @@ pub fn collect_files(
 
         Ok(WalkBuilder::new(path)
             .git_ignore(false)
-            .hidden(false)
+            .hidden(true)
             .overrides(combined_overrides)
             .build()
             .filter_map(|entry| entry.ok())