Feat(testing): Add coverage macro attributes and streamline testing config for faster testing

.config/nextest.toml

@@ -0,0 +1,28 @@
+# Nextest configuration for submod
+#
+# With per-test git config isolation (GIT_CONFIG_GLOBAL/GIT_CONFIG_SYSTEM),
+# tests are safe to run in parallel. The serial-integration group is kept as
+# defense-in-depth: integration tests that create repos, add/remove submodules,
+# and shell out to git are serialized among themselves to avoid any residual
+# contention on shared git state (e.g. lock files in /tmp).
+
+[test-groups]
+serial-integration = { max-threads = 1 }
+
+[profile.default]
+fail-fast = false
+
+# Integration tests that create/modify git repos run serially within their
+# group. config_tests and command_contract_tests are safe to run in parallel
+# with everything (they use isolated temp dirs and per-test gitconfig).
+[[profile.default.overrides]]
+filter = 'binary_id(submod::integration_tests) | binary_id(submod::sparse_checkout_tests) | binary_id(submod::error_handling_tests) | binary_id(submod::performance_tests)'
+test-group = 'serial-integration'
+
+# CI profile: fail fast but still serialize integration tests
+[profile.ci]
+fail-fast = true
+
+[[profile.ci.overrides]]
+filter = 'binary_id(submod::integration_tests) | binary_id(submod::sparse_checkout_tests) | binary_id(submod::error_handling_tests) | binary_id(submod::performance_tests)'
+test-group = 'serial-integration'

.serena/.gitignore

@@ -0,0 +1,2 @@
+/cache
+/project.local.yml

.serena/project.yml

@@ -0,0 +1,138 @@
+# the name by which the project can be referenced within Serena
+project_name: "submod"
+
+
+# list of languages for which language servers are started; choose from:
+#   al                  bash                clojure             cpp                 csharp
+#   csharp_omnisharp    dart                elixir              elm                 erlang
+#   fortran             fsharp              go                  groovy              haskell
+#   java                julia               kotlin              lua                 markdown
+#   matlab              nix                 pascal              perl                php
+#   php_phpactor        powershell          python              python_jedi         r
+#   rego                ruby                ruby_solargraph     rust                scala
+#   swift               terraform           toml                typescript          typescript_vts
+#   vue                 yaml                zig
+#   (This list may be outdated. For the current list, see values of Language enum here:
+#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py
+#   For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
+# Note:
+#   - For C, use cpp
+#   - For JavaScript, use typescript
+#   - For Free Pascal/Lazarus, use pascal
+# Special requirements:
+#   Some languages require additional setup/installations.
+#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
+# When using multiple languages, the first language server that supports a given file will be used for that file.
+# The first language is the default language and the respective language server will be used as a fallback.
+# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
+languages:
+- rust
+
+# the encoding used by text files in the project
+# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
+encoding: "utf-8"
+
+# line ending convention to use when writing source files.
+# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
+# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
+line_ending:
+
+# The language backend to use for this project.
+# If not set, the global setting from serena_config.yml is used.
+# Valid values: LSP, JetBrains
+# Note: the backend is fixed at startup. If a project with a different backend
+# is activated post-init, an error will be returned.
+language_backend:
+
+# whether to use project's .gitignore files to ignore files
+ignore_all_files_in_gitignore: true
+
+# list of additional paths to ignore in this project.
+# Same syntax as gitignore, so you can use * and **.
+# Note: global ignored_paths from serena_config.yml are also applied additively.
+ignored_paths: []
+
+# whether the project is in read-only mode
+# If set to true, all editing tools will be disabled and attempts to use them will result in an error
+# Added on 2025-04-18
+read_only: false
+
+# list of tool names to exclude.
+# This extends the existing exclusions (e.g. from the global configuration)
+#
+# Below is the complete list of tools for convenience.
+# To make sure you have the latest list of tools, and to view their descriptions, 
+# execute `uv run scripts/print_tool_overview.py`.
+#
+#  * `activate_project`: Activates a project by name.
+#  * `check_onboarding_performed`: Checks whether project onboarding was already performed.
+#  * `create_text_file`: Creates/overwrites a file in the project directory.
+#  * `delete_lines`: Deletes a range of lines within a file.
+#  * `delete_memory`: Deletes a memory from Serena's project-specific memory store.
+#  * `execute_shell_command`: Executes a shell command.
+#  * `find_referencing_code_snippets`: Finds code snippets in which the symbol at the given location is referenced.
+#  * `find_referencing_symbols`: Finds symbols that reference the symbol at the given location (optionally filtered by type).
+#  * `find_symbol`: Performs a global (or local) search for symbols with/containing a given name/substring (optionally filtered by type).
+#  * `get_current_config`: Prints the current configuration of the agent, including the active and available projects, tools, contexts, and modes.
+#  * `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file.
+#  * `initial_instructions`: Gets the initial instructions for the current project.
+#     Should only be used in settings where the system prompt cannot be set,
+#     e.g. in clients you have no control over, like Claude Desktop.
+#  * `insert_after_symbol`: Inserts content after the end of the definition of a given symbol.
+#  * `insert_at_line`: Inserts content at a given line in a file.
+#  * `insert_before_symbol`: Inserts content before the beginning of the definition of a given symbol.
+#  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
+#  * `list_memories`: Lists memories in Serena's project-specific memory store.
+#  * `onboarding`: Performs onboarding (identifying the project structure and essential tasks, e.g. for testing or building).
+#  * `prepare_for_new_conversation`: Provides instructions for preparing for a new conversation (in order to continue with the necessary context).
+#  * `read_file`: Reads a file within the project directory.
+#  * `read_memory`: Reads the memory with the given name from Serena's project-specific memory store.
+#  * `remove_project`: Removes a project from the Serena configuration.
+#  * `replace_lines`: Replaces a range of lines within a file with new content.
+#  * `replace_symbol_body`: Replaces the full definition of a symbol.
+#  * `restart_language_server`: Restarts the language server, may be necessary when edits not through Serena happen.
+#  * `search_for_pattern`: Performs a search for a pattern in the project.
+#  * `summarize_changes`: Provides instructions for summarizing the changes made to the codebase.
+#  * `switch_modes`: Activates modes by providing a list of their names
+#  * `think_about_collected_information`: Thinking tool for pondering the completeness of collected information.
+#  * `think_about_task_adherence`: Thinking tool for determining whether the agent is still on track with the current task.
+#  * `think_about_whether_you_are_done`: Thinking tool for determining whether the task is truly completed.
+#  * `write_memory`: Writes a named memory (for future reference) to Serena's project-specific memory store.
+excluded_tools: []
+
+# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).
+# This extends the existing inclusions (e.g. from the global configuration).
+included_optional_tools: []
+
+# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
+# This cannot be combined with non-empty excluded_tools or included_optional_tools.
+fixed_tools: []
+
+# list of mode names to that are always to be included in the set of active modes
+# The full set of modes to be activated is base_modes + default_modes.
+# If the setting is undefined, the base_modes from the global configuration (serena_config.yml) apply.
+# Otherwise, this setting overrides the global configuration.
+# Set this to [] to disable base modes for this project.
+# Set this to a list of mode names to always include the respective modes for this project.
+base_modes:
+
+# list of mode names that are to be activated by default.
+# The full set of modes to be activated is base_modes + default_modes.
+# If the setting is undefined, the default_modes from the global configuration (serena_config.yml) apply.
+# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
+# This setting can, in turn, be overridden by CLI parameters (--mode).
+default_modes:
+
+# initial prompt for the project. It will always be given to the LLM upon activating the project
+# (contrary to the memories, which are loaded on demand).
+initial_prompt: ""
+
+# time budget (seconds) per tool call for the retrieval of additional symbol information
+# such as docstrings or parameter information.
+# This overrides the corresponding setting in the global configuration; see the documentation there.
+# If null or missing, use the setting from the global configuration.
+symbol_info_budget:
+
+# list of regex patterns which, when matched, mark a memory entry as read‑only.
+# Extends the list from the global configuration, merging the two lists.
+read_only_memory_patterns: []

CLAUDE.md

@@ -1,110 +1,93 @@
-<!--
-SPDX-FileCopyrightText: 2025 Adam Poulemanos <89049923+bashandbone@users.noreply.github.com>
-
-SPDX-License-Identifier: LicenseRef-PlainMIT OR MIT
--->
-
 # CLAUDE.md
 
 This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
 
-## Project Overview
-
-`submod` is a Rust CLI tool for managing git submodules with advanced sparse checkout support. It uses `gitoxide` and `git2` libraries for high-performance git operations, with fallbacks to CLI git commands when needed.
-
-## Development Commands
-
-### Building and Testing
-
-- `cargo build` - Build the project
-- `cargo test` - Run unit tests
-- `./scripts/run-tests.sh` - Run comprehensive integration test suite
-- `./scripts/run-tests.sh --verbose` - Run tests with detailed output
-- `./scripts/run-tests.sh --performance` - Include performance tests
-- `./scripts/run-tests.sh --filter <pattern>` - Run specific test modules
-
-### Linting and Formatting
-
-- `cargo fmt` - Format code
-- `cargo clippy` - Run linter
-- `hk run check` - Run pre-commit checks via hk tool
-- `hk run fix` - Run auto-fixable linters
-
-### Mise Tasks (if using mise)
-
-- `mise run build` or `mise run b` - Build the CLI
-- `mise run test` - Run automated tests
-- `mise run lint` - Lint with clippy
-- `mise run ci` - Run CI tasks (build, lint, test)
-
-### Testing Philosophy
-
-The project follows integration-first testing. Focus on testing complete workflows and outputs rather than implementation details. Tests are run serially (`RUST_TEST_THREADS=1`) to avoid git submodule race conditions.
+## Commands
+
+### Build & Run
+```bash
+cargo build                    # debug build
+cargo build --release          # release build
+mise run build                 # alias: mise run b
+```
+
+### Test
+```bash
+cargo nextest run --all-features --no-fail-fast         # run all tests (preferred)
+cargo test --test integration_tests                     # integration tests only
+cargo test --test command_contract_tests                # command contract tests only
+./scripts/run-tests.sh --verbose                        # comprehensive test runner with reporting
+./scripts/run-tests.sh --filter sparse_checkout         # filter to specific tests
+mise run test                                           # alias: mise run t (runs via hk)
+```
+
+Integration tests that modify git repos are serialized via nextest test groups (`.config/nextest.toml`); other tests run in parallel. Each test gets an isolated git config via `GIT_CONFIG_GLOBAL` so tests never race on `~/.gitconfig`. The test suite is integration-test-focused; unit tests are minimal by design.
+
+### Lint & Format
+```bash
+cargo fmt                      # format code
+cargo clippy --all-features    # lint
+hk run check                   # run all linters (fmt, clippy, deny, typos, pkl)
+hk fix                         # auto-fix where possible
+mise run lint                  # alias for hk run check
+```
+
+### Full CI
+```bash
+mise run ci                    # build + lint + test
+hk run ci                      # same via hk (uses --fail-fast for tests)
+```
+
+### Git Hooks
+Managed by `hk` (configured in `hk.pkl`). Pre-commit runs: cargo fmt, clippy, check, nextest, typos, cargo-deny, pkl eval. Hooks install automatically with `mise install`.
 
 ## Architecture
 
-### Core Modules
-
-- `src/main.rs` - CLI entry point, parses commands and dispatches to manager
-- `src/commands.rs` - Command-line argument definitions using clap
-- `src/config.rs` - TOML configuration parsing and submodule config management
-- `src/git_manager.rs` - Core submodule operations using gitoxide/git2
-- `src/lib.rs` - Library exports (not a stable API)
-
-### Configuration System
-
-- Uses TOML configuration files (default: `submod.toml`)
-- Supports global defaults with per-submodule overrides
-- Handles sparse checkout paths, git options, and submodule settings
-
-### Git Operations Strategy
-
-1. **Primary**: gitoxide library for performance
-2. **Fallback**: git2 library (optional feature `git2-support`)
-3. **Final fallback**: CLI git commands
-
-### Key Design Patterns
-
-- Error handling with `anyhow` for application errors, `thiserror` for library errors
-- Comprehensive documentation for all public APIs
-- Strict linting configuration with pedantic clippy settings
-- Integration tests over unit tests
+`submod` is a CLI tool for managing git submodules with TOML configuration and sparse checkout support. It exposes the library as `src/lib.rs` primarily for integration testing (the public API is not stable).
 
-## Configuration Files
+### Layer Stack
 
-### Key Files to Know
+```
+CLI (commands.rs + main.rs)
+    ↓ clap parsing
+GitManager (git_manager.rs)          ← high-level submodule operations
+    ↓ delegates to
+GitOpsManager (git_ops/mod.rs)       ← unified backend with automatic fallback
+    ├── GixOperations (git_ops/gix_ops.rs)     ← gitoxide (preferred)
+    ├── Git2Operations (git_ops/git2_ops.rs)   ← libgit2 (fallback)
+    └── Git CLI                               ← last resort (spawned via std::process)
+Config (config.rs)                   ← figment-based TOML config loading/saving
+```
 
-- `Cargo.toml` - Project configuration with strict linting rules
-- `hk.pkl` - Git hooks configuration (pre-commit, linting)
-- `mise.toml` - Development environment and task definitions
-- `sample_config/submod.toml` - Example configuration
-- `scripts/run-tests.sh` - Comprehensive test runner
+### Fallback Architecture
 
-### Test Structure
+The core design is a **gix-first, git2-fallback, CLI-last-resort** strategy, driven by the immaturity of gitoxide's submodule support. `GitOpsManager` wraps both backends behind the `GitOperations` trait and calls `try_with_fallback()` / `try_with_fallback_mut()` for every operation. When gix fails, it logs a warning and transparently retries with git2; `add_submodule` has an additional CLI fallback that also cleans up any partial state from the prior attempt.
 
-- `tests/integration_tests.rs` - Core functionality tests
-- `tests/config_tests.rs` - Configuration parsing tests
-- `tests/sparse_checkout_tests.rs` - Sparse checkout functionality
-- `tests/error_handling_tests.rs` - Error conditions and edge cases
-- `tests/performance_tests.rs` - Performance and stress tests
+After destructive operations (delete, nuke), `GitOpsManager::reopen()` must be called to refresh the in-memory repository state. git2 reopen errors are fatal; gix reopen errors are warnings only.
 
-## Working with the Codebase
+### Configuration
 
-### Before Making Changes
+`Config` uses [figment](https://docs.rs/figment) to load `submod.toml`. The schema has:
+- `[defaults]` → `SubmoduleDefaults` (global git options applied to all submodules)
+- `[<name>]` sections → `SubmoduleEntry` (per-submodule config, overrides defaults)
 
-1. Run `./scripts/run-tests.sh` to ensure tests pass
-2. Check code formatting with `cargo fmt --check`
-3. Run linter with `cargo clippy`
+`SubmoduleEntry` merges `SubmoduleGitOptions` (ignore, fetch_recurse, branch, update) with submodule-specific fields (path, url, sparse_paths, active, shallow). Options are serialized to/from git-config-compatible strings via the `options.rs` newtype wrappers (`SerializableIgnore`, `SerializableUpdate`, etc.).
 
-### When Adding Features
+### Key Conventions
 
-- Add integration tests to appropriate test modules
-- Update configuration parsing if new config options are added
-- Follow existing error handling patterns
-- Document public APIs thoroughly
+- **Unsafe code is forbidden** (`unsafe_code = "forbid"` in `Cargo.toml`)
+- Clippy is configured at `pedantic` + `nursery` warn level; `correctness` is deny
+- `missing_docs` is warn — public items need doc comments
+- `module_name_repetitions` and `too_many_lines` are allowed
+- All error handling uses `anyhow` for propagation and `thiserror` for defining error types
+- `simple_gix.rs` contains lightweight gix helpers used in `gix_ops.rs`
 
-### Code Quality Standards
+### Testing Approach
 
-- Unsafe code is forbidden (`unsafe_code = "forbid"`)
-- All warnings treated seriously with comprehensive clippy configuration
-- Focus on clear, descriptive naming and comprehensive error messages
+Integration tests in `tests/` use a `TestHarness` (in `tests/common/mod.rs`) that creates temporary git repos and invokes the compiled binary. Test files:
+- `integration_tests.rs` — end-to-end CLI behavior
+- `command_contract_tests.rs` — CLI command argument contracts
+- `config_tests.rs` — configuration parsing/serialization
+- `sparse_checkout_tests.rs` — sparse checkout behavior
+- `error_handling_tests.rs` — error conditions and messages
+- `performance_tests.rs` — benchmarks (uses criterion)