Refactor: Extract database layer into separate crate

[CamonZ]

Overview

This PR completes a comprehensive refactoring to extract the database layer into a separate crate within a Cargo workspace. The database layer can now be used independently of the CLI, improving modularity and enabling future extensibility (web API, TUI, etc.).

Architecture Changes

Before

code_search/
├── Cargo.toml
└── src/
    ├── main.rs
    ├── cli.rs
    ├── commands/    (27 commands)
    ├── queries/     (31 query modules)
    ├── types/
    ├── db.rs
    └── ...

After

code_search/
├── Cargo.toml (workspace)
├── db/          (library crate)
│   ├── Cargo.toml
│   └── src/
│       ├── lib.rs
│       ├── db.rs
│       ├── types/
│       ├── queries/        (31 modules)
│       ├── query_builders.rs
│       ├── fixtures/       (test-utils feature)
│       └── test_utils.rs   (test-utils feature)
└── cli/         (binary crate)
    ├── Cargo.toml
    └── src/
        ├── main.rs
        ├── cli.rs
        ├── commands/       (27 commands)
        ├── output.rs
        ├── utils.rs
        └── test_macros.rs

Completed Work (8 Tickets)

✅ Ticket 1: Workspace Foundation

• Created Cargo workspace with db and cli crates
• Set up workspace dependencies and package inheritance
• Configured resolver version 2

✅ Ticket 2: DB Crate Core

• Moved types/ (Call, FunctionRef, ModuleGroup, TraceResult, etc.)
• Moved db.rs (database connection and query utilities)
• Established public API surface in db/src/lib.rs

✅ Ticket 3: Query Builders

• Extracted ConditionBuilder and OptionalConditionBuilder from utils.rs
• Created db/src/query_builders.rs
• Added comprehensive tests and documentation

✅ Ticket 4: Query Modules Migration

• Moved all 31 query modules to db/src/queries/
• Updated imports: crate::types → crate::types
• Preserved all functionality and tests

✅ Ticket 5: Test Infrastructure

• Created test-utils feature flag
• Moved fixtures and test utilities to db crate
• Updated CLI tests to use db with test-utils feature

✅ Ticket 6: CLI Migration

• Migrated all CLI source files to cli/src/
• Moved all 27 command modules
• Updated package name to code_search

✅ Ticket 7: Import Updates

• Updated all imports: crate:: → db::
• Fixed 300+ import statements across 27+ commands
• Verified compilation with no errors

✅ Ticket 8: Validation & Cleanup

• Fixed broken tests (template paths)
• Enabled ignored doctest
• Applied clippy improvements (37 auto-fixes + 1 manual)
• Removed unused DFS parameter
• Deleted old src/ directory (231 files)
• Reduced clippy warnings from 41 to 15 (63% reduction)

Key Improvements

Modularity:

• Database layer is now a standalone library
• Clear separation of concerns: data access vs. presentation
• CLI depends on db, but db has no CLI dependencies

Testability:

• Test fixtures shared via feature flag
• Database tests run independently
• 533 total tests (492 CLI + 40 DB + 1 doctest)

Extensibility:

• Can build new interfaces (web API, TUI) using the db crate
• Database logic reusable across multiple frontends
• Foundation for future plugin system

Code Quality:

• Clippy warnings reduced 63%
• Proper dependency boundaries enforced
• Documentation improved (workspace structure, doctest enabled)

Test Results

All tests passing ✅

CLI tests:     492 passed
DB tests:      40 passed
Doctests:      1 passed, 1 ignored (intentional)
Total:         533 tests

Build Commands

cargo build                      # Build entire workspace
cargo build -p cli               # Build CLI only
cargo build -p db                # Build DB library only
cargo test                       # Run all tests
cargo test -p db                 # Test DB layer only
cargo test -p code_search        # Test CLI layer only
cargo run -p code_search -- --help   # Run CLI

Breaking Changes

None for end users - the CLI binary works identically. Internal module paths have changed for future development.

Documentation

• Updated CLAUDE.md with workspace structure
• Added build commands and architecture overview
• Documented dependency flow and testing approach

Related Files

• Workspace config: Cargo.toml
• DB crate: db/Cargo.toml, db/src/lib.rs
• CLI crate: cli/Cargo.toml, cli/src/main.rs
• Documentation: CLAUDE.md