docs: synchronize project documentation with codebase

Implements 3 deferred security tickets (TICKET-003, TICKET-007, TICKET-010)
and performs comprehensive documentation audit to eliminate drift between
code and docs.

Code changes:
- TICKET-003: Repository integration tests with testcontainers-go (50+ subtests)
- TICKET-007: CertificateService decomposition into RevocationSvc + CAOperationsSvc
- TICKET-010: Request body size limits via http.MaxBytesReader middleware
- Fix missing slog import in certificate.go after service decomposition

Documentation updates:
- README: Fix endpoint count (97→93), expand env var reference (15→39 vars)
- CLAUDE.md: Fix OpenAPI operation count (85→93), update file locations
- architecture.md: Add body size limits section, middleware chain ordering
- CONTRIBUTING.md: New contributor guide with architecture conventions,
  test patterns, middleware ordering, CI thresholds
- SECURITY_REMEDIATION.md: Removed from repo (moved to cowork, gitignored)
- Test files: Add doc comments to all new test files

Documentation that should exist but doesn't yet:
- Architecture diagrams (C4 model or similar)
- Threat model document
- Testing philosophy guide
- Disaster recovery runbook
- Upgrade guide (migration between versions)
- API versioning strategy document

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs/architecture.md

@@ -717,10 +717,27 @@ Audit recording is async (via goroutine) so it never blocks the HTTP response. I
 
 All shell-facing inputs (connector scripts, domain names, ACME tokens) are validated through `internal/validation/command.go` before reaching shell execution. `ValidateShellCommand()` denies all shell metacharacters. `ValidateDomainName()` enforces RFC 1123. `ValidateACMEToken()` restricts to base64url characters. The network scanner filters reserved IP ranges (loopback, link-local including cloud metadata 169.254.169.254, multicast, broadcast) to prevent SSRF, while preserving RFC 1918 private ranges for legitimate internal scanning.
 
+### Request Body Size Limits
+
+All incoming HTTP request bodies are capped by `http.MaxBytesReader` middleware (default 1MB, configurable via `CERTCTL_MAX_BODY_SIZE`). Requests exceeding the limit receive a 413 Request Entity Too Large response. The middleware is positioned before authentication in the chain so oversized payloads are rejected early, before any auth processing or database work occurs. Requests without bodies (GET, HEAD, nil body) skip the limit check.
+
 ### CORS
 
 CORS uses a **deny-by-default** posture: when `CERTCTL_CORS_ORIGINS` is empty, no CORS headers are set and only same-origin requests can read responses. Operators must explicitly configure allowed origins. This prevents accidental exposure of the API to cross-origin requests in production.
 
+### Middleware Chain Order
+
+The HTTP middleware stack processes requests in the following order (see `cmd/server/main.go`):
+
+1. **RequestID** - assigns unique request ID for correlation
+2. **Logging** - structured slog middleware with request ID propagation
+3. **Recovery** - panic recovery (catches panics in downstream middleware/handlers)
+4. **BodyLimit** - request body size cap via `http.MaxBytesReader`
+5. **RateLimiter** - token bucket rate limiting (optional, when enabled)
+6. **CORS** - cross-origin request handling (deny-by-default)
+7. **Auth** - API key or JWT validation
+8. **AuditLog** - records every API call to the audit trail (requires auth context for actor)
+
 ### Concurrency Safety
 
 The background scheduler uses `sync/atomic.Bool` idempotency guards on all 6 loops — if a tick fires while the previous iteration is still running, it skips. A `sync.WaitGroup` tracks all in-flight goroutines. `WaitForCompletion(timeout)` blocks during shutdown until all work finishes or the timeout expires, preventing state corruption from mid-flight database operations during process exit.