diff --git a/PENTEST_PLAN.md b/PENTEST_PLAN.md
index 32ed2c6..a3cc548 100644
--- a/PENTEST_PLAN.md
+++ b/PENTEST_PLAN.md
@@ -251,16 +251,16 @@ Testing uses specialized Claude subagents for different security domains, with f
 ### Medium-term (Medium)
 
 - [ ] **HASH-001**: Add locking to content hash deduplication
-- [ ] **FLOOD-001**: Add memory limit to anti-flood request list
+- [x] **FLOOD-001**: Add memory limit to anti-flood request list
 - [ ] **ENUM-001**: Add rate limiting to paste metadata endpoints
-- [ ] **CLI-002**: Verify SSL certificate hostname matching
-- [ ] **CLI-003**: Add config file permission validation on startup
+- [x] **CLI-002**: Verify SSL certificate hostname matching
+- [x] **CLI-003**: Add config file permission validation on startup
+- [x] **AUDIT-001**: Add query result limits to prevent enumeration
 
 ### Long-term (Low)
 
 - [ ] **CRYPTO-001**: Add certificate serial collision detection
 - [ ] **TIMING-001**: Add constant-time database lookups for sensitive queries
-- [ ] **AUDIT-001**: Add query result limits to prevent enumeration
 
 ---
 
diff --git a/app/api/routes.py b/app/api/routes.py
index f78fa4b..259619a 100644
--- a/app/api/routes.py
+++ b/app/api/routes.py
@@ -98,11 +98,18 @@ def record_antiflood_request() -> None:
     decay = current_app.config["ANTIFLOOD_DECAY"]
     base = current_app.config["POW_DIFFICULTY"]
 
+    max_entries = current_app.config.get("ANTIFLOOD_MAX_ENTRIES", 10000)
+
     with _antiflood_lock:
         # Clean old requests
         cutoff = now - window
         _antiflood_requests[:] = [t for t in _antiflood_requests if t > cutoff]
 
+        # FLOOD-001: Cap list size to prevent memory exhaustion
+        if len(_antiflood_requests) >= max_entries:
+            # Keep only the most recent half
+            _antiflood_requests[:] = _antiflood_requests[-(max_entries // 2) :]
+
         # Record this request
         _antiflood_requests.append(now)
         count = len(_antiflood_requests)
diff --git a/app/config.py b/app/config.py
index 0fdc91f..452d9dd 100644
--- a/app/config.py
+++ b/app/config.py
@@ -84,6 +84,8 @@ class Config:
     ANTIFLOOD_STEP = int(os.environ.get("FLASKPASTE_ANTIFLOOD_STEP", "2"))  # bits per step
     ANTIFLOOD_MAX = int(os.environ.get("FLASKPASTE_ANTIFLOOD_MAX", "28"))  # max difficulty
     ANTIFLOOD_DECAY = int(os.environ.get("FLASKPASTE_ANTIFLOOD_DECAY", "60"))  # seconds to decay
+    # FLOOD-001: Maximum entries in anti-flood request list (memory DoS protection)
+    ANTIFLOOD_MAX_ENTRIES = int(os.environ.get("FLASKPASTE_ANTIFLOOD_MAX_ENTRIES", "10000"))
 
     # URL prefix for reverse proxy deployments (e.g., "/paste" for mymx.me/paste)
     URL_PREFIX = os.environ.get("FLASKPASTE_URL_PREFIX", "").rstrip("/")
diff --git a/fpaste b/fpaste
index d7ac0e6..9583eec 100755
--- a/fpaste
+++ b/fpaste
@@ -10,6 +10,7 @@ import json
 import os
 import shutil
 import ssl
+import stat
 import subprocess
 import sys
 import time
@@ -119,6 +120,11 @@ def die(msg: str, code: int = 1) -> NoReturn:
     sys.exit(code)
 
 
+def warn(msg: str) -> None:
+    """Print warning to stderr."""
+    print(f"warning: {msg}", file=sys.stderr)
+
+
 def request(
     url: str,
     method: str = "GET",
@@ -152,6 +158,20 @@ def parse_error(body: bytes, default: str = "request failed") -> str:
 # -----------------------------------------------------------------------------
 
 
+def check_config_permissions(path: Path) -> None:
+    """CLI-003: Warn if config file has insecure permissions."""
+    try:
+        mode = path.stat().st_mode
+        # Warn if group or others can read (should be 600 or 640)
+        if mode & stat.S_IROTH:
+            warn(f"config file {path} is world-readable (mode {stat.filemode(mode)})")
+        elif mode & stat.S_IRGRP:
+            # Group-readable is less severe, only warn if also has secrets
+            pass  # Silent for group-readable, common in shared setups
+    except OSError:
+        pass  # File may not exist yet or permission denied
+
+
 def read_config_file(path: Path | None = None) -> dict[str, str]:
     """Read config file and return key-value pairs."""
     path = path or CONFIG_FILE
@@ -160,6 +180,9 @@ def read_config_file(path: Path | None = None) -> dict[str, str]:
     if not path.exists():
         return result
 
+    # CLI-003: Check file permissions before reading
+    check_config_permissions(path)
+
     for line in path.read_text().splitlines():
         line = line.strip()
         if not line or line.startswith("#") or "=" not in line:
@@ -214,6 +237,10 @@ def create_ssl_context(config: Mapping[str, Any]) -> ssl.SSLContext | None:
         return None
 
     ctx = ssl.create_default_context()
+    # CLI-002: Explicitly enable hostname verification (defense in depth)
+    # create_default_context() sets these, but explicit is safer
+    ctx.check_hostname = True
+    ctx.verify_mode = ssl.CERT_REQUIRED
 
     if ca_cert := config.get("ca_cert", ""):
         ctx.load_verify_locations(ca_cert)