Make CLI-only distribution the supported path

[moinulmoin]

What changed

• make the Python CLI on PyPI the only supported Threadlens distribution
• remove PyInstaller, native release archives, npm shims, and platform packages
• keep Raycast as a thin UI over an installed threadlens command
• document the bundled SKILL.md and CLI-first installation clearly
• rewrite the main README around the user journey, supported sources, privacy, and integrations
• replace Raycast metadata screenshots and update vulnerable transitive dependencies
• prevent custom database/config paths from changing permissions on an existing parent directory
• prepare version 1.3.0 and remove stale V0 language across public documentation
• document migration from the discontinued npm/native builds

Why

Unsigned native executables create platform trust, signing, notarization, and maintenance costs that do not fit Threadlens. A stdlib-only Python CLI installed with uv or pipx keeps the product cross-platform without shipping opaque binaries. It also preserves the intended architecture: search lives in the CLI, while Raycast and agent skills remain thin clients.

The storage permission change closes a separate safety issue found during the documentation audit: Threadlens previously tightened permissions on any existing parent directory supplied through a custom path. It now applies private directory permissions only to directories it creates, while keeping the database/config file private.

User impact

• install with uv tool install threadlens or pipx install threadlens
• existing indexes remain compatible and rebuildable
• Raycast requires the CLI on PATH or an explicit command preference
• native/npm installation paths are no longer published or documented

Validation

• python3 -B -m py_compile threadlens/*.py
• python3 -B -m unittest discover -s tests — 134 tests passed
• TypeScript check passed
• Raycast lint and build passed
• npm audit reported 0 vulnerabilities
• doctor reported ready with all adapters healthy
• local eval: Recall@5 98%, 0 negative failures
• local benchmark: p95 156.9 ms under the 250 ms gate
• built and installed the 1.3.0 sdist and wheel
• verified both artifacts include SKILL.md and no npm/PyInstaller files