docs(env): sync .env lookup order to mention skill directory

Mirrors the config.py change from the prior commit. Seven doc sites
described the old three-step lookup order; refresh each one to insert
the skill-directory step between CWD and clone repo root, with an
example path so skill-install users know where their .env should sit.

Refs #136.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>