Separate Reflexio setup env from claude-smart runtime env

[wenchanghan]

Problem

claude-smart currently has a partial boundary between Reflexio setup state and claude-smart runtime state:

• Runtime services already load ~/.claude-smart/.env through REFLEXIO_ENV_FILE so a shared OSS Reflexio ~/.reflexio/.env cannot leak into claude-smart backend startup.
• The Python/Bash runtime path treats ~/.claude-smart/.env as the claude-smart runtime config file.
• Some setup surfaces still write claude-smart-specific keys into ~/.reflexio/.env, which makes the conceptual ownership boundary muddy and creates room for future host/config drift.

This is related to, but broader than, PR #99. PR #99 should stay focused on Windows/OpenCode first-try install behavior.

Current leaks to clean up

• bin/claude-smart.js: npm installer mirrors local defaults into both ~/.reflexio/.env and ~/.claude-smart/.env, including CLAUDE_SMART_HOST, CLAUDE_SMART_USE_LOCAL_CLI, CLAUDE_SMART_USE_LOCAL_EMBEDDING, and CLAUDE_SMART_READ_ONLY.
• scripts/setup-claude-smart.sh: interactive setup writes CLAUDE_SMART_READ_ONLY and local CLAUDE_SMART_* defaults into ~/.reflexio/.env.
• plugin/dashboard/lib/config-file.ts and the dashboard configure page read/write ~/.reflexio/.env for claude-smart runtime flags.
• README/Troubleshooting still describe claude-smart runtime flags under ~/.reflexio/.env in places.

Desired boundary

• ~/.reflexio/.env: Reflexio setup/connection state only, for example REFLEXIO_URL, REFLEXIO_API_KEY, and REFLEXIO_USER_ID.
• ~/.claude-smart/.env: claude-smart runtime/host/provider state, for example CLAUDE_SMART_HOST, CLAUDE_SMART_USE_LOCAL_CLI, CLAUDE_SMART_USE_LOCAL_EMBEDDING, CLAUDE_SMART_READ_ONLY, CLAUDE_SMART_OPENCODE_PATH, CLAUDE_SMART_CLI_PATH, and related runtime knobs.

Acceptance criteria

• Installers no longer generate host-specific CLAUDE_SMART_* runtime keys in ~/.reflexio/.env.
• Setup/dashboard/docs all agree on which file owns each key.
• Legacy installs with CLAUDE_SMART_READ_ONLY=1 or other claude-smart keys in ~/.reflexio/.env are migrated or respected without silently changing behavior.
• Backend/dashboard startup continues to read the intended runtime config from ~/.claude-smart/.env.
• Tests cover local mode, managed mode, read-only mode, dashboard config writes, and at least one legacy migration case.

Notes

Do this separately from PR #99 to avoid expanding a Windows/OpenCode compatibility PR into cross-host setup/dashboard semantics.