Refactor: Remove TUI, Isolate CLI Flags, and Fix Core Bugs

[nmdra]

Description

This pull request implements the changes outlined in the codebase analysis report to optimize the NoteBrain CLI for agentic usage and fix core inconsistencies.

1. Interactive TUI Removal

• Removed all interactive TUI features ( components, spinners, live search, result browser).
• Deleted and directories.
• Pruned associated dependencies from and .
• Updated all related documentation (, , and references).

2. CLI Flag Scope Refactoring

• Isolated Ingest Flags: Moved out of into .
• Isolated Semantic/Chunk Display Flags: Extracted , , and from into a reusable struct, embedded only where necessary (, , ).
• Purified the struct to only contain universal flags.
• Re-architected output formatting in to explicitly rely on the newly defined chunk display flags without forcing defaults on commands that don't use them (e.g. , ).

3. Core Bug Fixes

• Ingestion Pipeline Default: Ensured defaults to in to enforce short-chunk skipping rules as intended. Fixed associated unit tests.
• Dead Code: Removed the orphaned package, consolidating completely on the CLI flag framework.
• FFI Stability: Replaced unsafe hard-coded pagination () with () in to prevent Chroma FFI crashes on large vaults.

All tests have been updated and are passing locally.