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>

internal/api/middleware/bodylimit.go

@@ -0,0 +1,38 @@
+package middleware
+
+import (
+	"net/http"
+)
+
+// BodyLimitConfig holds configuration for the body size limit middleware.
+type BodyLimitConfig struct {
+	MaxBytes int64 // Maximum request body size in bytes; 0 = use default (1MB)
+}
+
+// DefaultMaxBodySize is the default maximum request body size (1MB).
+const DefaultMaxBodySize int64 = 1 * 1024 * 1024
+
+// NewBodyLimit creates a middleware that limits request body size.
+// If the body exceeds the configured limit, the server returns 413 Request Entity Too Large.
+// This prevents clients from sending excessively large payloads that could cause
+// memory exhaustion or denial of service (CWE-400).
+func NewBodyLimit(cfg BodyLimitConfig) func(http.Handler) http.Handler {
+	maxBytes := cfg.MaxBytes
+	if maxBytes <= 0 {
+		maxBytes = DefaultMaxBodySize
+	}
+
+	return func(next http.Handler) http.Handler {
+		return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+			// Skip body limit for requests without bodies
+			if r.Body == nil || r.ContentLength == 0 {
+				next.ServeHTTP(w, r)
+				return
+			}
+
+			// Wrap the body with MaxBytesReader
+			r.Body = http.MaxBytesReader(w, r.Body, maxBytes)
+			next.ServeHTTP(w, r)
+		})
+	}
+}