diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8e50d15..9c5ba46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 ## Unreleased
 
+- Fixed per-VM `DVM_CODE_ROOT` overrides so the default `DVM_CODE_DIR` is computed
+  after VM config is sourced.
+- Fixed remaining user-facing docs and diagnostics that still used old command names
+  after the `sync` / `sh` / `log` rename.
 - Renamed commands for shorter typing: `apply` → `sync`, `enter` → `sh`, `logs` →
   `log`, `list` → `ls`. The per-project hook moved from `.dvm/apply.sh` to
   `.dvm/sync.sh`; rename the file in projects that use it.
@@ -19,6 +23,18 @@
 - Moved `DVM_CHEZMOI_REPO`, `DVM_CHEZMOI_SIGNING_KEY`, and `DVM_CHEZMOI_DEPLOY_KEY` to
   global config; per-VM config only opts in via `use chezmoi` (per-VM override still
   works through the source order).
+- Tightened CLI arg validation: `init`, `sync`, `sh`, `ssh-key`, `gpg-key`, `ls`, and
+  `stop` now reject unexpected extra arguments with a clear error rather than
+  silently ignoring them.
+- Tightened `dvm rm` dirty check: when `git` is not installed in the guest, the
+  check now exits with status 2 and refuses to delete the VM unless `--force` is
+  passed. Previously the check exited cleanly when `git` was absent, allowing
+  silent deletion of un-checked code directories.
+- Extended `dvm rm` dirty check to also count files under `DVM_CODE_DIR` that are
+  not enclosed by any `.git` tree; the count and a sample of paths are printed and
+  deletion is refused unless `--force` is passed. Previously only dirty Git repos
+  blocked deletion; loose data files (databases, notes, downloads) could be lost
+  silently.
 - Added a `bat` recipe that installs bat from Fedora and runs `bat cache --build`.
 - Added VM config validation before Lima template rendering for VM names, users, sizing,
   code directories, host IPs, and port forwards.
diff --git a/SECURITY.md b/SECURITY.md
index 524686e..7dd4166 100644
--- a/SECURITY.md
+++ b/SECURITY.md
@@ -25,12 +25,12 @@ Defaults:
 - `~` in DVM config means the guest user's home
 - AI tools run inside the VM through `dvm-agent` when the recipe is used
 - public dotfiles use HTTPS by default
-- Cloudflare tokens are passed to apply explicitly, staged through a mode `0600` guest
+- Cloudflare tokens are passed to sync explicitly, staged through a mode `0600` guest
   temp file, and written inside the VM
 - forwarded ports bind to `127.0.0.1` unless config says otherwise
 - `dvm rm --yes` checks nested Git repos before deleting unless `--force` is used
 
-Most apply-time DVM environment values are visible to host process listings while
+Most sync-time DVM environment values are visible to host process listings while
 `limactl` runs. Do not put secrets in general `DVM_*` config. The bundled cloudflared
 token handoff is special-cased so `CLOUDFLARED_TOKEN` and `DVM_CLOUDFLARED_TOKEN` are
 not passed as `limactl shell env` arguments.
diff --git a/bin/dvm b/bin/dvm
index dedff31..330de5e 100755
--- a/bin/dvm
+++ b/bin/dvm
@@ -44,23 +44,28 @@ main() {
 	local cmd="${1:-help}"
 	[ "$#" -eq 0 ] || shift
 	case "$cmd" in
-	init) init_vm "$@" ;;
+	init)
+		case "$#" in
+		1 | 2) init_vm "$@" ;;
+		*) die "init takes <name> [template]" ;;
+		esac
+		;;
 	sync)
 		case "${1:-}" in
-		--all) apply_all ;;
+		--all) [ "$#" -eq 1 ] || die "sync --all takes no other arguments"; apply_all ;;
 		'') die "sync requires a VM name or --all" ;;
-		*) apply_one "$1" ;;
+		*) [ "$#" -eq 1 ] || die "sync takes one VM name"; apply_one "$1" ;;
 		esac
 		;;
-	sh) [ -n "${1:-}" ] || die "sh requires a VM name"; enter_vm "$1" ;;
+	sh) [ "$#" -eq 1 ] || die "sh takes one VM name"; enter_vm "$1" ;;
 	ssh) [ -n "${1:-}" ] || die "ssh requires a VM name"; ssh_vm "$@" ;;
 	cp) cp_vm "$@" ;;
-	log) logs_vm "$@" ;;
-	ssh-key) ssh_key_vm "$@" ;;
-	gpg-key) gpg_key_vm "$@" ;;
-	ls) list_vms ;;
-	stop) stop_vm "$@" ;;
-	rm) rm_vm "$@" ;;
+	log) [ "$#" -ge 1 ] || die "log requires a VM name"; logs_vm "$@" ;;
+	ssh-key) [ "$#" -eq 1 ] || die "ssh-key takes one VM name"; ssh_key_vm "$@" ;;
+	gpg-key) [ "$#" -eq 1 ] || die "gpg-key takes one VM name"; gpg_key_vm "$@" ;;
+	ls) [ "$#" -eq 0 ] || die "ls takes no arguments"; list_vms ;;
+	stop) [ "$#" -eq 1 ] || die "stop takes one VM name"; stop_vm "$@" ;;
+	rm) [ "$#" -ge 1 ] || die "rm requires a VM name"; rm_vm "$@" ;;
 	help | -h | --help) usage ;;
 	*) usage >&2; die "unknown command: $cmd" ;;
 	esac
diff --git a/docs/config.md b/docs/config.md
index 3d6a41b..9d9e22b 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -119,7 +119,7 @@ them from per-VM configs. Service recipes (`llama`, `cloudflared`) are not in
   `DVM_LLAMA_MODELS_SHA256`, `DVM_LLAMA_REFRESH`: llama model settings.
 - `DVM_CLOUDFLARED_SERVICE`, `DVM_CLOUDFLARED_TOKEN`: cloudflared service settings.
   The bundled cloudflared recipe receives the token through a mode `0600` guest temp
-  file during `apply`, so it is not passed as a `limactl shell env` argument.
+  file during `sync`, so it is not passed as a `limactl shell env` argument.
 - `DVM_NO_BASELINE=1`: skip the implicit `baseline` recipe. Service VMs use this to
   avoid dev-tool setup; recipes selected by that VM must install their own dependencies
   such as `git`, `curl`, `jq`, `tar`, or `unzip`.
diff --git a/docs/lima.md b/docs/lima.md
index c02cc77..c01a256 100644
--- a/docs/lima.md
+++ b/docs/lima.md
@@ -103,7 +103,7 @@ failed state after confirming the logs:
 dvm ssh app -- sudo systemctl reset-failed cloud-final.service cloud-init-main.service
 ```
 
-If Lima briefly misses an existing instance during `apply`, `ssh`, `enter`, or other DVM
+If Lima briefly misses an existing instance during `sync`, `ssh`, `sh`, or other DVM
 commands, DVM also checks the local Lima instance directory before deciding the VM is
 missing. If that local directory exists but `limactl start` cannot start it, DVM reports
 the likely stale instance directory path so you can inspect or remove it.
diff --git a/docs/security-standards.md b/docs/security-standards.md
index 94e6bc8..8c9a82f 100644
--- a/docs/security-standards.md
+++ b/docs/security-standards.md
@@ -22,9 +22,9 @@ small, but they are the bar for changes.
 - The VM-local GPG helper creates an unencrypted, one-year signing key for disposable
   VM use; do not treat it as a long-lived identity key.
 - Prefer repo-scoped deploy keys and service-scoped tokens.
-- Pass Cloudflare tokens only when applying the cloudflared VM, or fetch them from
-  macOS Keychain in your shell before apply.
-- Do not put secrets in general `DVM_*` config. Most apply-time DVM values are visible
+- Pass Cloudflare tokens only when syncing the cloudflared VM, or fetch them from
+  macOS Keychain in your shell before sync.
+- Do not put secrets in general `DVM_*` config. Most sync-time DVM values are visible
   to host process listings while `limactl` runs.
 - The bundled cloudflared token handoff is special-cased: `CLOUDFLARED_TOKEN` and
   `DVM_CLOUDFLARED_TOKEN` are staged through a mode `0600` guest temp file instead of
diff --git a/share/dvm/lib/core.sh b/share/dvm/lib/core.sh
index 9771223..0de68b9 100644
--- a/share/dvm/lib/core.sh
+++ b/share/dvm/lib/core.sh
@@ -224,7 +224,6 @@ load_vm() {
 	DVM_NAME="$name"
 	DVM_LIMA_NAME="${DVM_LIMA_NAME:-dvm-$name}"
 	DVM_CODE_ROOT="${DVM_CODE_ROOT:-~/code}"
-	DVM_CODE_DIR="${DVM_CODE_DIR:-${DVM_CODE_ROOT%/}/$name}"
 	DVM_PORTS="${DVM_PORTS:-}"
 	DVM_ARCH="${DVM_ARCH:-default}"
 	DVM_AI_AGENT_USER="${DVM_AI_AGENT_USER:-dvm-agent}"
diff --git a/share/dvm/lib/guest.sh b/share/dvm/lib/guest.sh
index 90184a2..93ee7bd 100644
--- a/share/dvm/lib/guest.sh
+++ b/share/dvm/lib/guest.sh
@@ -298,21 +298,21 @@ default_log_unit() {
 logs_vm() {
 	local name unit
 	name="${1:-}"
-	[ -n "$name" ] || die "logs requires a VM name"
+	[ -n "$name" ] || die "log requires a VM name"
 	shift || true
 	load_vm "$name"
 	vm_exists || die "VM does not exist: $DVM_LIMA_NAME; run dvm sync $name first"
 	start_vm
 	if [ "$#" -gt 0 ]; then
 		case "$1" in
-		-*) unit="$(default_log_unit)" || die "logs requires a unit when the VM has zero or multiple known service recipes" ;;
+		-*) unit="$(default_log_unit)" || die "log requires a unit when the VM has zero or multiple known service recipes" ;;
 		*)
 			unit="$1"
 			shift
 			;;
 		esac
 	else
-		unit="$(default_log_unit)" || die "logs requires a unit when the VM has zero or multiple known service recipes"
+		unit="$(default_log_unit)" || die "log requires a unit when the VM has zero or multiple known service recipes"
 	fi
 	if [ "$#" -eq 0 ]; then
 		set -- --no-pager -n 100
diff --git a/share/dvm/lib/vm_admin.sh b/share/dvm/lib/vm_admin.sh
index ff9dced..4cab505 100644
--- a/share/dvm/lib/vm_admin.sh
+++ b/share/dvm/lib/vm_admin.sh
@@ -10,7 +10,10 @@ case "$code_dir" in
 	"~/"*) code_dir="$HOME/${code_dir#\~/}" ;;
 esac
 [ -d "$code_dir" ] || exit 0
-command -v git >/dev/null 2>&1 || exit 0
+if ! command -v git >/dev/null 2>&1; then
+	printf 'dvm: dirty check skipped: git not installed in VM\n' >&2
+	exit 2
+fi
 dirty=0
 while IFS= read -r git_entry; do
 	if [ -d "$git_entry" ]; then
@@ -25,6 +28,29 @@ while IFS= read -r git_entry; do
 		dirty=1
 	fi
 done < <(find "$code_dir" \( -type d -name .git -prune -print \) -o \( -type f -name .git -print \))
+
+orphan_count=0
+orphan_sample=()
+while IFS= read -r f; do
+	orphan_count=$((orphan_count + 1))
+	if [ "${#orphan_sample[@]}" -lt 5 ]; then
+		orphan_sample+=("$f")
+	fi
+done < <(find "$code_dir" \
+	\( -type d -exec test -e {}/.git \; -prune \) -o \
+	\( -type d -name .git -prune \) -o \
+	\( -type f -print \) 2>/dev/null)
+
+if [ "$orphan_count" -gt 0 ]; then
+	printf 'dvm: %d file(s) outside any git repository under %s:\n' "$orphan_count" "$code_dir" >&2
+	for f in "${orphan_sample[@]}"; do
+		printf '  %s\n' "$f" >&2
+	done
+	if [ "$orphan_count" -gt "${#orphan_sample[@]}" ]; then
+		printf '  ... (%d more)\n' "$((orphan_count - ${#orphan_sample[@]}))" >&2
+	fi
+	dirty=1
+fi
 exit "$dirty"
 DVM_DIRTY_CHECK
 }
@@ -80,7 +106,14 @@ rm_vm() {
 		fi
 	fi
 	if [ "$force" != "1" ] && vm_exists && [ -f "$vm_file" ]; then
-		dirty_check_vm || die "refusing to delete $DVM_LIMA_NAME; commit/stash changes or pass --force"
+		local rc=0
+		dirty_check_vm || rc=$?
+		case "$rc" in
+		0) ;;
+		1) die "refusing to delete $DVM_LIMA_NAME; commit/stash changes, move untracked files, or pass --force" ;;
+		2) die "refusing to delete $DVM_LIMA_NAME; dirty check incomplete (see warning above), pass --force to skip" ;;
+		*) die "refusing to delete $DVM_LIMA_NAME; dirty check failed with status $rc, pass --force to skip" ;;
+		esac
 	elif [ "$force" != "1" ] && [ "$orphan" = "1" ]; then
 		printf 'dvm: warning: dirty check skipped because DVM config is missing: %s\n' "$vm_file" >&2
 	fi
diff --git a/tests/smoke.sh b/tests/smoke.sh
index d2265fa..d9e99ed 100755
--- a/tests/smoke.sh
+++ b/tests/smoke.sh
@@ -58,6 +58,15 @@ DVM_CODE_DIR="~/code/second"
 use python
 VM
 
+cat >"$TMP/config/vms/rooted.sh" <<'VM'
+DVM_CPUS=2
+DVM_MEMORY=4GiB
+DVM_DISK=20GiB
+DVM_CODE_ROOT="~/work"
+
+use python
+VM
+
 cat >"$TMP/config/vms/cloudflared.sh" <<'VM'
 DVM_CPUS=2
 DVM_MEMORY=2GiB
@@ -192,6 +201,21 @@ status="$?"
 set -e
 [ "$status" -ne 0 ]
 grep -Fq 'missing VM template: missing-template' "$TMP/init-bad.err"
+
+set +e
+"$ROOT/bin/dvm" sync app trailing-garbage >/dev/null 2>"$TMP/sync-extra.err"
+status="$?"
+set -e
+[ "$status" -ne 0 ]
+grep -Fq 'sync takes one VM name' "$TMP/sync-extra.err"
+
+set +e
+"$ROOT/bin/dvm" ls extra >/dev/null 2>"$TMP/ls-extra.err"
+status="$?"
+set -e
+[ "$status" -ne 0 ]
+grep -Fq 'ls takes no arguments' "$TMP/ls-extra.err"
+
 rm -f "$TMP/config/vms/newapp.sh" "$TMP/config/vms/llama.sh"
 
 "$ROOT/bin/dvm" sync app 2>"$TMP/apply.err"
@@ -244,6 +268,10 @@ grep -Fq 'dvm project hook' "$TMP/state/guest.sh"
 grep -Fq 'hostPort: 3000' "$TMP/state/lima.yaml"
 bash -n "$TMP/state/guest.sh"
 
+: >"$TMP/state/log"
+"$ROOT/bin/dvm" sync rooted
+grep -Fq 'DVM_CODE_DIR=~/work/rooted' "$TMP/state/log"
+
 : >"$TMP/state/log"
 CLOUDFLARED_TOKEN="smoke.Token_123=-" "$ROOT/bin/dvm" sync cloudflared
 grep -Fq 'dvm-cloudflared-token.' "$TMP/state/guest.sh"