Add staging, tags, remotes, three-way merges, fsck and expand CLI

[WorkofAditya]

Motivation

• Provide a richer VCS feature set including staging/index, lightweight tags, local remotes, and proper three-way merges with conflict handling.
• Make commits more robust (explicit parents list, snapshot handling) and add repository integrity checks and remote sync primitives.
• Improve user workflow with add, reset, revert, tag, fetch/push/pull, clone, and merge lifecycle commands (--continue/--abort).

Description

• Implement a persistent staging index and merge state stored in .leaf/index.json and .leaf/MERGE_STATE.json and add helper APIs in Modules/storage.py (load_index, save_index, load_merge_state, save_merge_state, clear_merge_state, etc.).
• Enhance commit creation to support explicit parents arrays, create full snapshot for the first commit, support staged commits (apply index to base state), and write commit objects and states via _create_commit, _write_commit_files, and related helpers in Modules/commands.py.
• Add three-way merge logic with conflict markers, merge base calculation, and merge lifecycle commands leaf_merge, leaf_merge_continue, and leaf_merge_abort, plus helper merge functions and find_merge_base in Modules/graph.py.
• Add index commands leaf_add and leaf_reset, tagging with leaf_tag, local remotes with leaf_remote/leaf_fetch/leaf_push/leaf_pull, leaf_clone, leaf_revert, and leaf_fsck for repository integrity checks, and wire them into the CLI entrypoint (leaf).
• Refactor storage to atomic JSON saves (_atomic_json_save) and robust loaders (_load_json, safe_load_log) and improve rebuild logic (first_parent_chain) and working-tree write error handling.
• Update status, log, diff, checkout, restore flows to account for staging and merge state, clear index/merge state where appropriate, and surface tags and merge parents in logs and status outputs.

Testing

• Added a comprehensive integration-style test suite tests/test_leaf_cli.py exercising init/save/branch/checkout/fast-forward and three-way merges, conflict handling (--continue/--abort), staging, reset, tag, revert, fsck, and remote fetch/push/pull/clone workflows.
• Ran the test suite with pytest (including the new tests/test_leaf_cli.py) and all tests completed successfully.

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Codex Task