New commands: add and add-from-fs

[tony]

Changes

New: Added vcspull fmt

• Introduces a fmt subcommand to normalize configuration files (sort directories/repos, convert compact entries to verbose {repo: ...} form, and standardize keys).
• Example: uv run vcspull fmt --config ~/.vcspull.yaml --write

New: Added vcspull add

• Adds a single repository entry to the configuration with flexible base directory detection.
• Example: uv run vcspull add myrepo git@github.com:user/myrepo.git --dir ~/code

New: Added vcspull add-from-fs

• Scans a directory (optionally recursively) for git repositories and appends new entries to the configuration, prompting for confirmation unless --yes is specified.
• Example: uv run vcspull add-from-fs ~/study/typescript --config ~/.vcspull.yaml --yes

Logging Improvements

• Replace the import-time NullHandler with a configured stdout StreamHandler to restore CLI output after the logging refactor.
• Ensure handlers survive pytest stream rotation via safe flush/reset logic.
• Added regression test test_add_from_fs_stream_output to guarantee user-facing output remains visible.

Config & CLI Enhancements

• ConfigReader now reads files using UTF-8 explicitly.
• Shared helper save_config_yaml centralizes YAML writes with UTF-8 encoding.
• CLI parser now wires in the new subcommands and routes to dedicated modules.

Fixes: #25, #333

Testing

• uv run ruff check src/vcspull/log.py tests/cli/test_add_from_fs.py
• uv run mypy
• uv run py.test

Additional Notes

• Extensive new CLI tests cover add/add-from-fs/fmt behaviors, including duplicate detection, confirmation prompts, and formatting summaries.
• Logging test suite expanded to validate handler configuration, propagation, and formatter integration.

[sourcery-ai]

Reviewer's Guide

This pull request introduces two new CLI subcommands, add and add-from-fs, to vcspull, enhancing its repository management capabilities. The add command is implemented in src/vcspull/cli/add.py and allows users to manually specify repository details (URL, name, target path) for addition to the YAML configuration. The add-from-fs command, housed in src/vcspull/cli/add_from_fs.py, scans a specified filesystem directory for Git repositories, automatically extracts their remote 'origin' URLs, and adds them to the configuration, optionally after user confirmation. Both functionalities are integrated into the main CLI by updating src/vcspull/cli/__init__.py to include new argument subparsers and modify the command dispatch logic. This involved refactoring create_parser to manage and return a collection of all subparsers and updating the cli function to robustly pass arguments to the respective command handlers.

File-Level Changes

Change	Details	Files
Implemented add command for manual repository addition to the configuration.	Created add.py module with logic to parse repository details (URL, name, path) and update the YAML configuration. Defined command-line arguments for the add subparser within add.py. Integrated the add subparser and its handler into the main CLI structure in __init__.py.	src/vcspull/cli/add.py src/vcspull/cli/__init__.py
Implemented add-from-fs command to discover local Git repositories and add them to the configuration.	Created add_from_fs.py module with logic to scan directories, extract Git remote URLs, and update the configuration, including an interactive confirmation step. Defined command-line arguments for the add-from-fs subparser within add_from_fs.py. Integrated the add-from-fs subparser and its handler into the main CLI structure in __init__.py.	src/vcspull/cli/add_from_fs.py src/vcspull/cli/__init__.py
Refactored CLI argument parsing and command dispatching in __init__.py.	Modified create_parser function to support the registration and retrieval of multiple subparsers. Updated the main cli function to correctly dispatch to the new command handlers based on the invoked subparser. Improved argument handling when calling command handlers by checking for attribute existence on the parsed arguments object.	src/vcspull/cli/__init__.py

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[codecov]

Codecov Report

❌ Patch coverage is 72.43902% with 113 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.70%. Comparing base (60d3f70) to head (c5dfc5e).

Files with missing lines	Patch %	Lines
src/vcspull/cli/add_from_fs.py	70.37%	29 Missing and 11 partials ⚠️
src/vcspull/cli/fmt.py	74.80%	20 Missing and 13 partials ⚠️
src/vcspull/cli/add.py	60.00%	23 Missing and 7 partials ⚠️
src/vcspull/log.py	87.30%	3 Missing and 5 partials ⚠️
src/vcspull/cli/sync.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #465      +/-   ##
==========================================
- Coverage   78.93%   76.70%   -2.24%     
==========================================
  Files           8       11       +3     
  Lines         413      807     +394     
  Branches       85      184      +99     
==========================================
+ Hits          326      619     +293     
- Misses         52      119      +67     
- Partials       35       69      +34     

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