Clarify human and agent setup

[moinulmoin]

Summary

• restructure the main README around separate agent-managed and human-managed setup paths
• add a copy-paste agent prompt with explicit install, permission, privacy, and approval boundaries
• align the bundled skill and Raycast guide with the same diagnostics and least-privilege guidance
• link the now-live Threadlens Raycast Store page

Validation

• python3 -B -m py_compile threadlens/*.py
• python3 -B -m unittest discover -s tests (134 tests)
• npm --prefix raycast exec -- tsc --project raycast/tsconfig.json --noEmit
• npm --prefix raycast audit --json (0 vulnerabilities)
• npm --prefix raycast run lint
• npm --prefix raycast run build
• python3 -B -m threadlens doctor --json
• local retrieval eval: 98% Recall@5, 0 negative failures
• local search benchmark: 159.6 ms p95 (250 ms gate)

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Use the installer that owns the existing installation

When Threadlens is already installed by pipx but uv is also available, this procedure directs the agent to run uv tool upgrade threadlens; that command only upgrades uv-installed tools (uv tool upgrade --help describes it as “Upgrade installed tools”) and exits with “threadlens is not installed” in this scenario. Detect whether the resolved command belongs to uv or pipx and use the corresponding upgrade command so an otherwise valid existing installation does not derail setup.

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[chatgpt-codex-connector]

Avoid promising permission errors that doctor cannot discover

When access is denied while traversing a standard session directory—the permission problem this section is intended to diagnose—source_paths() returns only files it successfully discovers, while inaccessible glob roots and failed .exists() candidates are omitted. Consequently cmd_doctor() can report the source as ok (0/0) with no path or read error, so users cannot follow this troubleshooting advice; explicitly probe and report candidate roots or document that doctor cannot identify this class of denial.

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