feat: add fail-closed phase gate enforcement system

- phase-config.yml: Phase dependency graph (source of truth)
- phase-enforce.yml: 5-layer enforcement engine with retry/backoff
- bypass-audit.yml: Emergency bypass audit trail
- ARCHITECTURE.md: Full threat model and decision matrix
- configure-branch-protection.sh: One-shot setup script
- Updated PR template with bypass reason section

Pattern lineage: eight-eyes/circuit_breaker → squad-audit/label-enforce

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: Brian Krafft

.github/phase-config.yml

@@ -0,0 +1,78 @@
+# Phase Gate Dependency Configuration
+# =====================================
+# This file defines the dependency graph between project phases.
+# Milestone names in GitHub MUST match the phase names here exactly.
+#
+# Enforcement workflow reads this file on every PR event.
+# Changes to this file require a PR (enforced by branch protection).
+#
+# Dependency Graph:
+#
+#                 P0 (Emergency Hardening)
+#                / \
+#               /   \
+#              v     v
+#   P1 (Foundation)  P2 (Smart Sandbox)
+#      |                  |
+#      v                  |
+#   P3 (store.py)         |
+#      |                  |
+#      v                  |
+#   P4 (tool+mcp)         |
+#      |                  |
+#      v                  v
+#      P5 (evolver+grounding) <--+
+#         |
+#         v
+#      P6 (Production Readiness)
+#         |
+#         v
+#      P7 (Enforcement & Launch)
+
+phases:
+  "Phase 0 — Emergency Hardening":
+    prerequisites: []
+    description: "Stop the bleeding — critical security, error handling, env hygiene"
+
+  "Phase 1 — Foundation Architecture":
+    prerequisites:
+      - "Phase 0 — Emergency Hardening"
+    description: "Hexagonal skeleton, DI container, type system, CI foundation"
+
+  "Phase 2 — Smart Sandbox":
+    prerequisites:
+      - "Phase 0 — Emergency Hardening"
+    description: "E2B integration, capability leases, 9-stage pre-execution pipeline"
+
+  "Phase 3 — Extract store.py":
+    prerequisites:
+      - "Phase 1 — Foundation Architecture"
+    description: "Decompose store.py god-class into 7 focused modules"
+
+  "Phase 4 — Extract tool_layer + mcp_server":
+    prerequisites:
+      - "Phase 3 — Extract store.py"
+    description: "Decompose tool_layer.py (6 modules) and mcp_server.py (5 modules)"
+
+  "Phase 5 — Extract evolver + grounding":
+    prerequisites:
+      - "Phase 2 — Smart Sandbox"
+      - "Phase 4 — Extract tool_layer + mcp_server"
+    description: "Decompose evolver.py (9 modules) and grounding_agent.py (8 modules)"
+
+  "Phase 6 — Production Readiness":
+    prerequisites:
+      - "Phase 5 — Extract evolver + grounding"
+    description: "Observability, SLOs, deployment architecture, DX polish"
+
+  "Phase 7 — Enforcement & Launch":
+    prerequisites:
+      - "Phase 6 — Production Readiness"
+    description: "Eight-eyes integration, SkillGuard, launch checklist"
+
+# Escape hatch configuration
+escape_hatch:
+  label: "emergency:bypass"
+  require_reason: true
+  reason_pattern: "## Bypass Reason"
+  min_reason_length: 10

.github/pull_request_template.md

@@ -22,3 +22,9 @@ Closes #<!-- issue number -->
 ## 📝 ADR
 - [ ] No architecture decisions made
 - [ ] ADR written: `docs/adr/ADR-XXX.md`
+
+<!--
+## Bypass Reason
+(Delete this section unless using emergency:bypass label)
+(Explain why this PR must skip phase gate enforcement)
+-->

.github/workflows/bypass-audit.yml

@@ -0,0 +1,122 @@
+# ============================================================================
+# Emergency Bypass Audit — Track and report all enforcement overrides
+# ============================================================================
+#
+# Fires when the `emergency:bypass` label is added or removed.
+# Creates a persistent audit record as a repo issue with the `audit` label.
+# Also removes the bypass label after merge to prevent re-use.
+
+name: Bypass Audit Trail
+
+on:
+  pull_request:
+    types: [closed, labeled]
+    branches: [main]
+
+permissions:
+  contents: read
+  issues: write
+  pull-requests: write
+
+jobs:
+  # Record when bypass label is applied
+  audit-bypass-applied:
+    if: >
+      github.event.action == 'labeled' &&
+      github.event.label.name == 'emergency:bypass'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Record bypass activation
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const pr = context.payload.pull_request;
+            const actor = context.actor;
+
+            // Extract bypass reason from PR body
+            const body = pr.body || '';
+            const reasonIdx = body.indexOf('## Bypass Reason');
+            let reason = '(No reason provided)';
+            if (reasonIdx !== -1) {
+              reason = body.slice(reasonIdx + '## Bypass Reason'.length).trim().split('\n')[0];
+            }
+
+            // Create audit issue
+            await github.rest.issues.create({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              title: `🔓 Bypass Activated: PR #${pr.number} by @${actor}`,
+              body: [
+                `## Emergency Bypass Audit Record`,
+                ``,
+                `| Field | Value |`,
+                `|-------|-------|`,
+                `| **PR** | #${pr.number} |`,
+                `| **Title** | ${pr.title} |`,
+                `| **Actor** | @${actor} |`,
+                `| **Timestamp** | ${new Date().toISOString()} |`,
+                `| **Reason** | ${reason} |`,
+                `| **PR Labels** | ${pr.labels.map(l => '`' + l.name + '`').join(', ')} |`,
+                ``,
+                `> This record was auto-generated by the bypass audit system.`,
+                `> Bypass records are permanent and cannot be deleted.`,
+              ].join('\n'),
+              labels: ['audit', 'emergency:bypass'],
+            });
+
+            core.info(`📝 Audit record created for bypass on PR #${pr.number}`);
+
+  # Clean up bypass label after merge + create completion record
+  audit-bypass-merged:
+    if: >
+      github.event.action == 'closed' &&
+      github.event.pull_request.merged == true &&
+      contains(github.event.pull_request.labels.*.name, 'emergency:bypass')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Record bypass merge and clean up
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const pr = context.payload.pull_request;
+
+            // Remove the bypass label so it can't be re-used if PR is reopened
+            try {
+              await github.rest.issues.removeLabel({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: pr.number,
+                name: 'emergency:bypass',
+              });
+              core.info('Removed emergency:bypass label from merged PR');
+            } catch (err) {
+              core.warning(`Could not remove bypass label: ${err.message}`);
+            }
+
+            // Find the audit issue for this PR and add merge note
+            const auditIssues = await github.rest.issues.listForRepo({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              labels: 'audit,emergency:bypass',
+              state: 'open',
+            });
+
+            const auditIssue = auditIssues.data.find(i =>
+              i.title.includes(`PR #${pr.number}`)
+            );
+
+            if (auditIssue) {
+              await github.rest.issues.createComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: auditIssue.number,
+                body: [
+                  `## ✅ Bypass Merge Complete`,
+                  ``,
+                  `PR #${pr.number} was merged at ${new Date().toISOString()}.`,
+                  `Merge commit: ${pr.merge_commit_sha}`,
+                  ``,
+                  `This audit record will remain open for 30-day review.`,
+                ].join('\n'),
+              });
+            }