Feature/unifies contree home

[mosquito]

This pull request introduces several improvements and refactors to the CLI, focusing on configuration flexibility, file upload efficiency, and enhanced logging for debugging. The main highlights are the addition of a new cli.ini configuration for user defaults, parallelized file uploads with local caching, and more detailed HTTP request/response logging.

Configuration and Defaults:

• Added support for a cli.ini configuration file (CliSettings) to allow users to specify CLI defaults such as log_level, output_format, and preferred editor. These defaults are loaded and applied at startup, and the editor default is now used in file editing commands. ([[1]](https://github.com/nebius/contree-cli/pull/2/files#diff-388aa0832650292b5e85f0e5e60d494a00b91251c9144995882b0b118afb4440R1-R41), [[2]](https://github.com/nebius/contree-cli/pull/2/files#diff-3bdb1edae3c4e48dd7da3e83d7ba06f36031b0f4f510fd08e6da2f9919733f10L11-R11), [[3]](https://github.com/nebius/contree-cli/pull/2/files#diff-3bdb1edae3c4e48dd7da3e83d7ba06f36031b0f4f510fd08e6da2f9919733f10R24-R32), [[4]](https://github.com/nebius/contree-cli/pull/2/files#diff-ef53e076b15ba1e03353742592511c277797e36c02543c183080571ae1d3369bR31), [[5]](https://github.com/nebius/contree-cli/pull/2/files#diff-ef53e076b15ba1e03353742592511c277797e36c02543c183080571ae1d3369bL181-R183))

File Uploads and Caching:

• Refactored the file upload logic to support parallel uploads using a thread pool, with improved local caching of file UUIDs to avoid redundant uploads. The cache now persists host file to UUID mappings and reuses them if within the retention period. ([[1]](https://github.com/nebius/contree-cli/pull/2/files#diff-e1d1d59d05ce4ab826c18d37bde2c867f834f5c05afe057e52eefa84c42f70dbL354-R432), [[2]](https://github.com/nebius/contree-cli/pull/2/files#diff-e1d1d59d05ce4ab826c18d37bde2c867f834f5c05afe057e52eefa84c42f70dbL537-R575))

• Updated the file upload implementation to stream files directly from disk (using file handles) instead of reading all bytes into memory, improving efficiency and reducing memory usage. ([[1]](https://github.com/nebius/contree-cli/pull/2/files#diff-ef53e076b15ba1e03353742592511c277797e36c02543c183080571ae1d3369bL131-R136), [[2]](https://github.com/nebius/contree-cli/pull/2/files#diff-e1d1d59d05ce4ab826c18d37bde2c867f834f5c05afe057e52eefa84c42f70dbL354-R432))

Logging and Debugging:

• Introduced a BodyFormatter class and enhanced HTTP request/response logging. Now logs request and response bodies in detail (with truncation for large/binary data), and logs errors with more context. Added a BufferedResponse helper for replaying buffered responses in debug mode. ([[1]](https://github.com/nebius/contree-cli/pull/2/files#diff-6eeb005451cd1cb39243b4499164f5b6eea61a03dbd4efa655351147bd921710R38-R124), [[2]](https://github.com/nebius/contree-cli/pull/2/files#diff-6eeb005451cd1cb39243b4499164f5b6eea61a03dbd4efa655351147bd921710L83-R172), [[3]](https://github.com/nebius/contree-cli/pull/2/files#diff-6eeb005451cd1cb39243b4499164f5b6eea61a03dbd4efa655351147bd921710R188-R194), [[4]](https://github.com/nebius/contree-cli/pull/2/files#diff-6eeb005451cd1cb39243b4499164f5b6eea61a03dbd4efa655351147bd921710L109-R213), [[5]](https://github.com/nebius/contree-cli/pull/2/files#diff-6eeb005451cd1cb39243b4499164f5b6eea61a03dbd4efa655351147bd921710R229-R230), [[6]](https://github.com/nebius/contree-cli/pull/2/files#diff-6eeb005451cd1cb39243b4499164f5b6eea61a03dbd4efa655351147bd921710R242-R250), [[7]](https://github.com/nebius/contree-cli/pull/2/files#diff-6eeb005451cd1cb39243b4499164f5b6eea61a03dbd4efa655351147bd921710R262-R295))

Command Handling and Robustness:

• Improved command dispatch logic to correctly distinguish between commands that require a remote client/profile and those that operate purely locally (such as auth, agent, man, skill). ([contree_cli/__main__.pyL41-R62](https://github.com/nebius/contree-cli/pull/2/files#diff-3bdb1edae3c4e48dd7da3e83d7ba06f36031b0f4f510fd08e6da2f9919733f10L41-R62))

• Added fatal logging for failed operations in cmd_run, providing clear feedback when remote operations do not succeed. ([contree_cli/cli/run.pyR709-R716](https://github.com/nebius/contree-cli/pull/2/files#diff-e1d1d59d05ce4ab826c18d37bde2c867f834f5c05afe057e52eefa84c42f70dbR709-R716))

Command Argument Handling:

• Improved shell command argument quoting using shlex.join and shlex.quote to ensure safe and accurate command construction in both shell and non-shell modes. ([[1]](https://github.com/nebius/contree-cli/pull/2/files#diff-e1d1d59d05ce4ab826c18d37bde2c867f834f5c05afe057e52eefa84c42f70dbL406-R447), [[2]](https://github.com/nebius/contree-cli/pull/2/files#diff-e1d1d59d05ce4ab826c18d37bde2c867f834f5c05afe057e52eefa84c42f70dbL421-R459))

These changes collectively improve usability, reliability, and debuggability of the CLI.