fix: harden enter/stop and WAL recovery

- Guard WAL recovery and stale .running cleanup behind a try-acquired store lock\n- Persist rollback ResetState via MetadataStore to recompute checksums\n- Track a killable host PID for namespace enter/stop and treat SIGTERM/SIGKILL as clean exit\n- Derive OCI status PID via runtime state output\n- Make sandbox chroot script quoting robust for exec/enter

crates/karapace-cli/src/commands/new.rs

@@ -4,7 +4,7 @@ use karapace_schema::manifest::{
     parse_manifest_str, BaseSection, GuiSection, HardwareSection, ManifestV1, MountsSection,
     RuntimeSection, SystemSection,
 };
-use std::io::{stdin, IsTerminal};
+use std::io::{stderr, stdin, IsTerminal};
 use std::path::{Path, PathBuf};
 use tempfile::NamedTempFile;
 
@@ -87,12 +87,14 @@ fn print_result(name: &str, template: Option<&str>, json: bool) -> Result<(), St
 
 pub fn run(name: &str, template: Option<&str>, force: bool, json: bool) -> Result<u8, String> {
     let dest = Path::new(DEST_MANIFEST);
-    let is_tty = stdin().is_terminal();
-    ensure_can_write(dest, force, is_tty)?;
+    let is_tty = stdin().is_terminal() && stderr().is_terminal();
 
     let mut manifest = if let Some(tpl) = template {
-        load_template(tpl)?
+        let m = load_template(tpl)?;
+        ensure_can_write(dest, force, is_tty)?;
+        m
     } else {
+        ensure_can_write(dest, force, is_tty)?;
         if !is_tty {
             return Err("no --template provided and stdin is not a TTY".to_owned());
         }

crates/karapace-cli/src/commands/stop.rs

@@ -1,12 +1,8 @@
 use super::{resolve_env_id_pretty, EXIT_SUCCESS};
-use karapace_core::{Engine, StoreLock};
-use karapace_store::StoreLayout;
+use karapace_core::Engine;
 use std::path::Path;
 
-pub fn run(engine: &Engine, store_path: &Path, env_id: &str) -> Result<u8, String> {
-    let layout = StoreLayout::new(store_path);
-    let _lock = StoreLock::acquire(&layout.lock_file()).map_err(|e| format!("store lock: {e}"))?;
-
+pub fn run(engine: &Engine, _store_path: &Path, env_id: &str) -> Result<u8, String> {
     let resolved = resolve_env_id_pretty(engine, env_id)?;
     engine.stop(&resolved).map_err(|e| e.to_string())?;
     println!("stopped environment {env_id}");

crates/karapace-core/src/engine.rs

@@ -56,27 +56,39 @@ impl Engine {
         let layer_store = LayerStore::new(layout.clone());
         let wal = WriteAheadLog::new(&layout);
 
-        // Recover any incomplete operations from a previous crash
-        if let Err(e) = wal.recover() {
-            warn!("WAL recovery failed: {e}");
-        }
+        // Recovery mutates the store and must not run concurrently with a live
+        // operation holding the store lock (e.g. an interactive `enter`).
+        match StoreLock::try_acquire(&layout.lock_file()) {
+            Ok(Some(_lock)) => {
+                // Recover any incomplete operations from a previous crash
+                if let Err(e) = wal.recover() {
+                    warn!("WAL recovery failed: {e}");
+                }
 
-        // Clean up stale .running markers left by a crash during enter/exec.
-        // After WAL recovery, any env still marked Running was mid-operation.
-        let env_base = layout.env_dir();
-        if env_base.exists() {
-            if let Ok(entries) = std::fs::read_dir(&env_base) {
-                for entry in entries.flatten() {
-                    let running_marker = entry.path().join(".running");
-                    if running_marker.exists() {
-                        debug!(
-                            "removing stale .running marker: {}",
-                            running_marker.display()
-                        );
-                        let _ = std::fs::remove_file(&running_marker);
+                // Clean up stale .running markers left by a crash during enter/exec.
+                // After WAL recovery, any env still marked Running was mid-operation.
+                let env_base = layout.env_dir();
+                if env_base.exists() {
+                    if let Ok(entries) = std::fs::read_dir(&env_base) {
+                        for entry in entries.flatten() {
+                            let running_marker = entry.path().join(".running");
+                            if running_marker.exists() {
+                                debug!(
+                                    "removing stale .running marker: {}",
+                                    running_marker.display()
+                                );
+                                let _ = std::fs::remove_file(&running_marker);
+                            }
+                        }
                     }
                 }
             }
+            Ok(None) => {
+                debug!("store lock held; skipping WAL recovery and stale marker cleanup");
+            }
+            Err(e) => {
+                warn!("store lock check failed; skipping WAL recovery: {e}");
+            }
         }
 
         let store_root_str = root.to_string_lossy().into_owned();

crates/karapace-remote/src/http.rs

@@ -1,4 +1,5 @@
 use crate::{BlobKind, RemoteBackend, RemoteConfig, RemoteError};
+use std::io::Read;
 
 /// HTTP-based remote store backend.
 ///
@@ -56,9 +57,10 @@ impl HttpBackend {
             req = req.header("Authorization", &format!("Bearer {token}"));
         }
         let resp = req.call().map_err(|e| RemoteError::Http(e.to_string()))?;
-        let body = resp
-            .into_body()
-            .read_to_vec()
+        let mut reader = resp.into_body().into_reader();
+        let mut body = Vec::new();
+        reader
+            .read_to_end(&mut body)
             .map_err(|e| RemoteError::Http(e.to_string()))?;
         Ok(body)
     }
@@ -195,7 +197,7 @@ mod tests {
 
                         let mut body = vec![0u8; content_length];
                         if content_length > 0 {
-                            let _ = std::io::Read::read_exact(&mut reader, &mut body);
+                            let _ = reader.read_exact(&mut body);
                         }
 
                         let mut data = store.lock().unwrap();

crates/karapace-runtime/src/namespace.rs

@@ -5,12 +5,14 @@ use crate::image::{
     parse_version_output, query_versions_command, resolve_image, ImageCache,
 };
 use crate::sandbox::{
-    enter_interactive, exec_in_container, install_packages_in_container, mount_overlay,
-    setup_container_rootfs, unmount_overlay, SandboxConfig,
+    exec_in_container, install_packages_in_container, mount_overlay, setup_container_rootfs,
+    spawn_enter_interactive, unmount_overlay, SandboxConfig,
 };
 use crate::terminal;
 use crate::RuntimeError;
 use karapace_schema::{ResolutionResult, ResolvedPackage};
+use libc::{SIGKILL, SIGTERM};
+use std::os::unix::process::ExitStatusExt;
 use std::path::{Path, PathBuf};
 
 pub struct NamespaceBackend {
@@ -237,13 +239,8 @@ impl RuntimeBackend for NamespaceBackend {
 
         // Mount overlay
         mount_overlay(&sandbox)?;
-
-        // Set up rootfs
         setup_container_rootfs(&sandbox)?;
 
-        // Mark as running
-        std::fs::write(env_dir.join(".running"), format!("{}", std::process::id()))?;
-
         // Emit terminal markers
         terminal::emit_container_push(&spec.env_id, &sandbox.hostname);
         terminal::print_container_banner(
@@ -252,8 +249,38 @@ impl RuntimeBackend for NamespaceBackend {
             &sandbox.hostname,
         );
 
-        // Enter the container interactively
-        let exit_code = enter_interactive(&sandbox);
+        // Spawn the sandbox so we can record the host PID for `stop`.
+        let mut child = match spawn_enter_interactive(&sandbox) {
+            Ok(c) => c,
+            Err(e) => {
+                terminal::emit_container_pop();
+                terminal::print_container_exit(&spec.env_id);
+                let _ = unmount_overlay(&sandbox);
+                return Err(e);
+            }
+        };
+
+        if let Err(e) = std::fs::write(env_dir.join(".running"), format!("{}", child.id())) {
+            let _ = child.kill();
+            terminal::emit_container_pop();
+            terminal::print_container_exit(&spec.env_id);
+            let _ = unmount_overlay(&sandbox);
+            return Err(e.into());
+        }
+
+        // Wait for the interactive session to complete.
+        let exit_code = match child.wait() {
+            Ok(status) => {
+                let code = status.code().unwrap_or_else(|| match status.signal() {
+                    Some(sig) if sig == SIGTERM || sig == SIGKILL => 0,
+                    _ => 1,
+                });
+                Ok(code)
+            }
+            Err(e) => Err(RuntimeError::ExecFailed(format!(
+                "failed to wait for sandbox: {e}"
+            ))),
+        };
 
         // Cleanup
         terminal::emit_container_pop();

crates/karapace-runtime/src/oci.rs

@@ -11,7 +11,7 @@ use crate::sandbox::{
 use crate::terminal;
 use crate::RuntimeError;
 use karapace_schema::{ResolutionResult, ResolvedPackage};
-use std::path::{Path, PathBuf};
+use std::path::PathBuf;
 use std::process::Command;
 
 pub struct OciBackend {
@@ -451,35 +451,45 @@ impl RuntimeBackend for OciBackend {
     }
 
     fn status(&self, env_id: &str) -> Result<RuntimeStatus, RuntimeError> {
-        let env_dir = self.env_dir(env_id);
-        let running_file = env_dir.join(".running");
+        let runtime = Self::find_runtime().ok_or_else(|| {
+            RuntimeError::BackendUnavailable("no OCI runtime found (crun/runc/youki)".to_owned())
+        })?;
 
-        if running_file.exists() {
-            let pid_str = std::fs::read_to_string(&running_file).unwrap_or_default();
-            let pid = pid_str.trim().parse::<u32>().ok();
-            if pid.is_none() && !pid_str.trim().is_empty() {
-                tracing::warn!(
-                    "corrupt .running file for {}: could not parse PID from '{}'",
-                    &env_id[..12.min(env_id.len())],
-                    pid_str.trim()
-                );
-            }
-            if let Some(p) = pid {
-                if Path::new(&format!("/proc/{p}")).exists() {
-                    return Ok(RuntimeStatus {
-                        env_id: env_id.to_owned(),
-                        running: true,
-                        pid: Some(p),
-                    });
-                }
-                let _ = std::fs::remove_file(&running_file);
+        let container_id = format!("karapace-{}", &env_id[..12.min(env_id.len())]);
+        let output = Command::new(&runtime)
+            .args(["state", &container_id])
+            .output()?;
+
+        if !output.status.success() {
+            let stderr = String::from_utf8_lossy(&output.stderr);
+            let msg = stderr.to_lowercase();
+            if msg.contains("does not exist") || msg.contains("not found") {
+                return Ok(RuntimeStatus {
+                    env_id: env_id.to_owned(),
+                    running: false,
+                    pid: None,
+                });
             }
+            return Err(RuntimeError::ExecFailed(format!(
+                "{runtime} state failed: {}",
+                stderr.trim()
+            )));
         }
 
+        let state: serde_json::Value = serde_json::from_slice(&output.stdout).map_err(|e| {
+            RuntimeError::ExecFailed(format!("failed to parse {runtime} state output: {e}"))
+        })?;
+
+        let pid = state
+            .get("pid")
+            .and_then(serde_json::Value::as_u64)
+            .and_then(|p| u32::try_from(p).ok())
+            .filter(|p| *p != 0);
+
         Ok(RuntimeStatus {
             env_id: env_id.to_owned(),
-            running: false,
-            pid: None,
+            running: pid.is_some(),
+            pid,
         })
     }
 }

crates/karapace-runtime/src/sandbox.rs

@@ -248,7 +248,14 @@ fn ensure_user_in_container(config: &SandboxConfig, merged: &Path) -> Result<(),
 
 fn build_unshare_command(config: &SandboxConfig) -> Command {
     let mut cmd = Command::new("unshare");
-    cmd.args(["--user", "--map-root-user", "--mount", "--pid", "--fork"]);
+    cmd.args([
+        "--user",
+        "--map-root-user",
+        "--mount",
+        "--pid",
+        "--fork",
+        "--kill-child=SIGTERM",
+    ]);
 
     if config.isolate_network {
         cmd.arg("--net");
@@ -343,7 +350,7 @@ fn build_setup_script(config: &SandboxConfig) -> String {
     }
 
     // Chroot and exec
-    let _ = write!(script, "exec chroot {qm} /bin/sh -c '");
+    let _ = writeln!(script, "exec chroot {qm} /bin/sh -s <<'__KARAPACE_EOF__'");
 
     script
 }
@@ -409,7 +416,10 @@ pub fn enter_interactive(config: &SandboxConfig) -> Result<i32, RuntimeError> {
         "/bin/sh"
     };
 
-    let _ = write!(setup, "{env_exports}cd ~; exec {shell} -l'");
+    let _ = write!(
+        setup,
+        "{env_exports}cd ~; exec {shell} -l </dev/tty >/dev/tty 2>/dev/tty\n__KARAPACE_EOF__\n"
+    );
 
     let mut cmd = build_unshare_command(config);
     cmd.arg("/bin/sh").arg("-c").arg(&setup);
@@ -426,6 +436,86 @@ pub fn enter_interactive(config: &SandboxConfig) -> Result<i32, RuntimeError> {
     Ok(status.code().unwrap_or(1))
 }
 
+pub fn spawn_enter_interactive(
+    config: &SandboxConfig,
+) -> Result<std::process::Child, RuntimeError> {
+    let merged = &config.overlay_merged;
+
+    let mut setup = build_setup_script(config);
+
+    // Build environment variable exports (all values shell-quoted, keys validated)
+    let mut env_exports = String::new();
+    for (key, val) in &config.env_vars {
+        if !key.bytes().all(|b| b.is_ascii_alphanumeric() || b == b'_') {
+            continue; // Skip keys with unsafe characters
+        }
+        let _ = write!(env_exports, "export {}={}; ", key, shell_quote(val));
+    }
+
+    // Set standard env vars (all values shell-quoted)
+    let _ = write!(
+        env_exports,
+        "export HOME={}; ",
+        shell_quote_path(&config.home_dir)
+    );
+    let _ = write!(
+        env_exports,
+        "export USER={}; ",
+        shell_quote(&config.username)
+    );
+    let _ = write!(
+        env_exports,
+        "export HOSTNAME={}; ",
+        shell_quote(&config.hostname)
+    );
+    if let Ok(xdg) = std::env::var("XDG_RUNTIME_DIR") {
+        let _ = write!(
+            env_exports,
+            "export XDG_RUNTIME_DIR={}; ",
+            shell_quote(&xdg)
+        );
+    }
+    if let Ok(display) = std::env::var("DISPLAY") {
+        let _ = write!(env_exports, "export DISPLAY={}; ", shell_quote(&display));
+    }
+    if let Ok(wayland) = std::env::var("WAYLAND_DISPLAY") {
+        let _ = write!(
+            env_exports,
+            "export WAYLAND_DISPLAY={}; ",
+            shell_quote(&wayland)
+        );
+    }
+    env_exports.push_str("export TERM=${TERM:-xterm-256color}; ");
+    let _ = write!(
+        env_exports,
+        "export KARAPACE_ENV=1; export KARAPACE_HOSTNAME={}; ",
+        shell_quote(&config.hostname)
+    );
+
+    // Determine shell
+    let shell = if merged.join("bin/bash").exists() || merged.join("usr/bin/bash").exists() {
+        "/bin/bash"
+    } else {
+        "/bin/sh"
+    };
+
+    let _ = write!(
+        setup,
+        "{env_exports}cd ~; exec {shell} -l </dev/tty >/dev/tty 2>/dev/tty\n__KARAPACE_EOF__\n"
+    );
+
+    let mut cmd = build_unshare_command(config);
+    cmd.arg("/bin/sh").arg("-c").arg(&setup);
+
+    // Pass through stdin/stdout/stderr for interactive use
+    cmd.stdin(std::process::Stdio::inherit());
+    cmd.stdout(std::process::Stdio::inherit());
+    cmd.stderr(std::process::Stdio::inherit());
+
+    cmd.spawn()
+        .map_err(|e| RuntimeError::ExecFailed(format!("failed to spawn sandbox: {e}")))
+}
+
 pub fn exec_in_container(
     config: &SandboxConfig,
     command: &[String],
@@ -453,7 +543,11 @@ pub fn exec_in_container(
     env_exports.push_str("export KARAPACE_ENV=1; ");
 
     let escaped_cmd: Vec<String> = command.iter().map(|a| shell_quote(a)).collect();
-    let _ = write!(setup, "{env_exports}{}'", escaped_cmd.join(" "));
+    let _ = write!(
+        setup,
+        "{env_exports}{}\n__KARAPACE_EOF__\n",
+        escaped_cmd.join(" ")
+    );
 
     let mut cmd = build_unshare_command(config);
     cmd.arg("/bin/sh").arg("-c").arg(&setup);

crates/karapace-store/src/wal.rs

@@ -1,4 +1,5 @@
 use crate::layout::StoreLayout;
+use crate::metadata::{EnvMetadata, EnvState, MetadataStore};
 use crate::StoreError;
 use serde::{Deserialize, Serialize};
 use std::fs;
@@ -7,6 +8,17 @@ use std::path::PathBuf;
 use tempfile::NamedTempFile;
 use tracing::{debug, info, warn};
 
+fn parse_env_state(s: &str) -> Option<EnvState> {
+    match s {
+        "Defined" | "defined" => Some(EnvState::Defined),
+        "Built" | "built" => Some(EnvState::Built),
+        "Running" | "running" => Some(EnvState::Running),
+        "Frozen" | "frozen" => Some(EnvState::Frozen),
+        "Archived" | "archived" => Some(EnvState::Archived),
+        _ => None,
+    }
+}
+
 /// A single rollback step that can undo part of an operation.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum RollbackStep {
@@ -196,34 +208,50 @@ impl WriteAheadLog {
                     env_id,
                     target_state,
                 } => {
-                    // Resolve metadata dir from wal_dir (wal_dir = root/store/wal)
-                    if let Some(store_dir) = self.wal_dir.parent() {
-                        let metadata_dir = store_dir.join("metadata");
-                        let meta_path = metadata_dir.join(env_id);
-                        if meta_path.exists() {
-                            match fs::read_to_string(&meta_path) {
-                                Ok(content) => {
-                                    if let Ok(mut meta) =
-                                        serde_json::from_str::<serde_json::Value>(&content)
-                                    {
-                                        meta["state"] =
-                                            serde_json::Value::String(target_state.clone());
-                                        if let Ok(updated) = serde_json::to_string_pretty(&meta) {
-                                            if let Err(e) = fs::write(&meta_path, updated) {
-                                                warn!("WAL rollback: failed to reset state for {env_id}: {e}");
-                                            } else {
-                                                debug!("WAL rollback: reset {env_id} state to {target_state}");
-                                            }
-                                        }
-                                    }
-                                }
-                                Err(e) => {
-                                    warn!(
-                                        "WAL rollback: failed to read metadata for {env_id}: {e}"
-                                    );
-                                }
-                            }
+                    let Some(new_state) = parse_env_state(target_state) else {
+                        warn!("WAL rollback: unknown target state '{target_state}' for {env_id}");
+                        continue;
+                    };
+
+                    // wal_dir = <root>/store/wal
+                    let Some(store_dir) = self.wal_dir.parent() else {
+                        continue;
+                    };
+                    let Some(root_dir) = store_dir.parent() else {
+                        continue;
+                    };
+
+                    let meta_path = store_dir.join("metadata").join(env_id);
+                    if !meta_path.exists() {
+                        continue;
+                    }
+
+                    let content = match fs::read_to_string(&meta_path) {
+                        Ok(c) => c,
+                        Err(e) => {
+                            warn!("WAL rollback: failed to read metadata for {env_id}: {e}");
+                            continue;
                         }
+                    };
+
+                    let mut meta: EnvMetadata = match serde_json::from_str(&content) {
+                        Ok(m) => m,
+                        Err(e) => {
+                            warn!("WAL rollback: failed to parse metadata for {env_id}: {e}");
+                            continue;
+                        }
+                    };
+
+                    meta.state = new_state;
+                    meta.updated_at = chrono::Utc::now().to_rfc3339();
+                    meta.checksum = None;
+
+                    let layout = StoreLayout::new(root_dir);
+                    let meta_store = MetadataStore::new(layout);
+                    if let Err(e) = meta_store.put(&meta) {
+                        warn!("WAL rollback: failed to persist metadata for {env_id}: {e}");
+                    } else {
+                        debug!("WAL rollback: reset {env_id} state to {target_state}");
                     }
                 }
             }