• Added a new configuration option to copy local .env files into isolated worktrees for Scout MCP compatibility.
• Removed outdated note regarding Claude Code binary path from setup documentation.
• Renumbered subsequent steps in the setup guide for clarity.

Summary

Describe this PR in 2-5 bullets:

• Problem:
• Why it matters:
• What changed:
• What did not change (scope boundary):

UX Journey

Before

(Draw the user-facing flow BEFORE this PR. Show each step the user takes.)

Example:
  User                   Archon                   AI Client
  ────                   ──────                   ─────────
  sends message ──────▶  resolves session
                         loads context
                         streams to AI ──────────▶ processes prompt
                         receives chunks ◀──────── streams response
  sees reply ◀─────────  sends to platform

After

(Draw the user-facing flow AFTER this PR. Highlight what changed with [brackets] or asterisks.)

Architecture Diagram

Before

(Map ALL modules touched or connected to this change. Draw lines between them.)

After

(Same diagram with changes highlighted. Mark new modules with [+], removed with [-],
 modified with [~]. Mark new connections with ===, removed with --x--.)

Connection inventory (list every module-to-module edge, mark changes):

Label Snapshot

• Risk: risk: low|medium|high
• Size: size: XS|S|M|L|XL
• Scope: core|workflows|isolation|git|adapters|server|web|cli|paths|config|docs|dependencies|ci|tests|skills
• Module: <scope>:<component> (e.g. workflows:executor, adapters:slack, core:orchestrator)

Change Metadata

• Change type: bug|feature|refactor|docs|security|chore
• Primary scope: core|workflows|isolation|git|adapters|server|web|cli|paths|multi

Linked Issue

• Closes #
• Related #
• Depends on # (if stacked)
• Supersedes # (if replacing older PR)

Validation Evidence (required)

Commands and result summary:

bun run type-check
bun run lint
bun run format:check
bun run test
# Or all at once:
bun run validate

• Evidence provided (test/log/trace/screenshot):
• If any command is intentionally skipped, explain why:

Security Impact (required)

• New permissions/capabilities? (Yes/No)
• New external network calls? (Yes/No)
• Secrets/tokens handling changed? (Yes/No)
• File system access scope changed? (Yes/No)
• If any Yes, describe risk and mitigation:

Compatibility / Migration

• Backward compatible? (Yes/No)
• Config/env changes? (Yes/No)
• Database migration needed? (Yes/No)
• If yes, exact upgrade steps:

Human Verification (required)

What was personally validated beyond CI:

• Verified scenarios:
• Edge cases checked:
• What was not verified:

Side Effects / Blast Radius (required)

• Affected subsystems/workflows:
• Potential unintended effects:
• Guardrails/monitoring for early detection:

Rollback Plan (required)

• Fast rollback command/path:
• Feature flags or config toggles (if any):
• Observable failure symptoms:

Risks and Mitigations

List real risks in this PR (or write None).

• Risk:
  • Mitigation: