docs: address setup friction points and client config pitfalls (#123)

[dandye]

Resolves #123

Summary of Changes

This PR updates the setup, configuration, and troubleshooting documentation across README.md and docs/usage_guide.md to address common friction points encountered during first-time onboarding:

1. uv Installation & Desktop GUI Client PATH Gotchas:
   • Documented uv installation options.
   • Clarified why desktop GUI applications (Claude Desktop, Cursor, VS Code / Cline) often do not inherit shell profile PATH additions (e.g., ~/.local/bin/uv), resulting in spawn uv ENOENT.
   • Documented running which uv and specifying the full absolute path in "command".
2. Virtual Environment vs. Standalone uv:
   • Clarified that while using uv or Python from an existing virtual environment is supported, a standalone global uv installation is recommended because uv run handles per-server isolation automatically.
3. Directory Depth & Entrypoint Gotchas (The SCC Copy-Paste Trap):
   • Highlighted the entry point differences: SecOps, SOAR, and GTI run server.py from nested package directories (secops_mcp, secops_soar_mcp, gti_mcp), whereas SCC runs scc_mcp.py directly from server/scc/.
   • Added warnings against setting --directory to <repo>/server/ or copy-pasting server.py for SCC.
4. --env-file Flag Placement:
   • Documented that --env-file is a flag to uv run and must appear after run in the args array.
5. SOAR SSL Certificate Verification & certifi:
   • Documented CA certificate requirements for SecOps SOAR connections on macOS (Install Certificates.command and SSL_CERT_FILE with certifi).
6. Fallback Pattern (/bin/bash -c):
   • Provided an explicit /bin/bash -c fallback configuration example for environments where uv cannot be located by GUI desktop clients or when using existing virtual environments.