diff --git a/Cargo.lock b/Cargo.lock
index 382a7b32..27d2b3b8 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -84,6 +84,7 @@ dependencies = [
  "flate2",
  "hex",
  "insta",
+ "libc",
  "pbkdf2",
  "ponytail",
  "pretty_assertions",
diff --git a/Cargo.toml b/Cargo.toml
index 5079b68d..c72bfc4a 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -71,6 +71,9 @@ agentflare-backend = { package = "agentflare-backend", path = "crates/agentflare
 db_kit = { package = "agentflare-db-kit", path = "crates/agentflare-db-kit" }
 agent-detector = "0.2.1"
 
+[target.'cfg(unix)'.dependencies]
+libc = "0.2"
+
 [features]
 default = []
 process-tree = ["sysinfo"]
diff --git a/src/alias.rs b/src/alias.rs
index 6bb1a82f..bc9aae84 100644
--- a/src/alias.rs
+++ b/src/alias.rs
@@ -292,7 +292,8 @@ fn write_managed_block(
             end += 1;
         }
         let new_content = content[..start].to_string() + &new_block + &content[end..];
-        std::fs::write(profile, new_content)?;
+        crate::atomic_fs::write_bytes_with_fallback(profile, new_content.as_bytes(), None)
+            .map_err(std::io::Error::other)?;
         return Ok(());
     }
 
@@ -301,7 +302,8 @@ fn write_managed_block(
         new_content.push('\n');
     }
     new_content.push_str(&new_block);
-    std::fs::write(profile, new_content)?;
+    crate::atomic_fs::write_bytes_with_fallback(profile, new_content.as_bytes(), None)
+        .map_err(std::io::Error::other)?;
     Ok(())
 }
 
diff --git a/src/atomic_fs.rs b/src/atomic_fs.rs
new file mode 100644
index 00000000..38aa289b
--- /dev/null
+++ b/src/atomic_fs.rs
@@ -0,0 +1,303 @@
+//! Shared, policy-free atomic-write mechanics.
+//!
+//! agentflare writes files whose truncation on a crash mid-write would be a
+//! real problem — auth vault credential files (`auth.rs`) and the user's own
+//! shell profile (`alias.rs`'s managed alias block) — using plain
+//! `fs::write`, which is not crash-atomic: a process killed between the
+//! `open` and the `write` completing leaves a truncated (or zero-byte) file
+//! in place of the original.
+//!
+//! This module provides one audited mechanism: a same-directory temp file +
+//! `rename`, with an in-place-overwrite fallback when the directory is
+//! read-only but the file inode itself is writable. Ported from lean-ctx's
+//! `core/atomic_fs.rs`.
+
+use std::borrow::Cow;
+use std::path::Path;
+use std::time::{SystemTime, UNIX_EPOCH};
+
+fn invalid_input(msg: &'static str) -> std::io::Error {
+    std::io::Error::new(std::io::ErrorKind::InvalidInput, msg)
+}
+
+/// Resolves one level of symlink indirection so an atomic write lands on the
+/// real file `path` points at, not on a new plain file replacing the symlink
+/// itself — `rename()` does not follow a symlink destination, it unlinks it
+/// and puts the new file in its place. A relative link target is resolved
+/// against the symlink's own parent directory. Non-symlinks (and symlinks
+/// this can't stat, e.g. a dangling one) pass through unchanged.
+fn resolve_symlink_target(path: &Path) -> Cow<'_, Path> {
+    let Ok(meta) = std::fs::symlink_metadata(path) else {
+        return Cow::Borrowed(path);
+    };
+    if !meta.file_type().is_symlink() {
+        return Cow::Borrowed(path);
+    }
+    let Ok(target) = std::fs::read_link(path) else {
+        return Cow::Borrowed(path);
+    };
+    if target.is_absolute() {
+        Cow::Owned(target)
+    } else {
+        let parent = path.parent().unwrap_or_else(|| Path::new("."));
+        Cow::Owned(parent.join(target))
+    }
+}
+
+/// Durable, crash-atomic write: a temp file in the **same directory** as `path`
+/// (after resolving one level of symlink, so a symlinked target is written
+/// through rather than replaced) followed by `rename` over the target.
+/// Requires write permission on the parent directory; the read-only-directory
+/// fallback is handled by [`write_bytes_with_fallback`].
+///
+/// When `permissions` is `None` and the target already exists, its current
+/// permissions are carried over to the replacement — otherwise the new inode
+/// would get the process's default (umask-masked) mode, silently loosening
+/// e.g. a `0600` credential file to world-readable.
+pub fn try_atomic_write(
+    path: &Path,
+    bytes: &[u8],
+    permissions: Option<&std::fs::Permissions>,
+) -> std::io::Result<()> {
+    use std::io::Write;
+
+    let resolved = resolve_symlink_target(path);
+    let path: &Path = &resolved;
+
+    let parent = path
+        .parent()
+        .ok_or_else(|| invalid_input("invalid path (no parent directory)"))?;
+    let filename = path
+        .file_name()
+        .ok_or_else(|| invalid_input("invalid path (no filename)"))?
+        .to_string_lossy();
+
+    let owned_perms;
+    let permissions = match permissions {
+        Some(p) => Some(p),
+        None => {
+            owned_perms = std::fs::metadata(path).ok().map(|m| m.permissions());
+            owned_perms.as_ref()
+        }
+    };
+
+    let pid = std::process::id();
+    let nanos = SystemTime::now()
+        .duration_since(UNIX_EPOCH)
+        .map_or(0, |d| d.as_nanos());
+    let tmp = parent.join(format!(".{filename}.agentflare.tmp.{pid}.{nanos}"));
+
+    {
+        let mut f = std::fs::OpenOptions::new()
+            .write(true)
+            .create_new(true)
+            .open(&tmp)?;
+        f.write_all(bytes)?;
+        let _ = f.flush();
+        let _ = f.sync_all();
+    }
+
+    if let Some(perms) = permissions {
+        let _ = std::fs::set_permissions(&tmp, perms.clone());
+    }
+
+    // std::fs::rename already replaces an existing destination on every
+    // platform we build for (including Windows, via MoveFileExW's
+    // MOVEFILE_REPLACE_EXISTING) — no separate pre-removal needed, and one
+    // would only open a window where neither the old nor new file exists.
+    if let Err(e) = std::fs::rename(&tmp, path) {
+        // Don't leave a half-written temp behind before the caller decides
+        // whether to fall back.
+        let _ = std::fs::remove_file(&tmp);
+        return Err(e);
+    }
+    Ok(())
+}
+
+/// In-place overwrite of an existing file inode (`O_WRONLY|O_TRUNC`, plus
+/// `O_NOFOLLOW` on Unix). Works when the parent directory is read-only but the
+/// file itself is writable. Not crash-atomic — used only as a fallback when the
+/// atomic path is impossible.
+pub fn in_place_overwrite(
+    path: &Path,
+    bytes: &[u8],
+    permissions: Option<&std::fs::Permissions>,
+) -> std::io::Result<()> {
+    use std::io::Write;
+
+    let mut opts = std::fs::OpenOptions::new();
+    opts.write(true).truncate(true);
+    #[cfg(unix)]
+    {
+        use std::os::unix::fs::OpenOptionsExt;
+        // O_NOFOLLOW: a symlink swapped in after the caller's checks must never
+        // be followed here.
+        opts.custom_flags(libc::O_NOFOLLOW);
+    }
+
+    let mut f = opts.open(path)?;
+    f.write_all(bytes)?;
+    let _ = f.flush();
+    let _ = f.sync_all();
+
+    if let Some(perms) = permissions {
+        let _ = std::fs::set_permissions(path, perms.clone());
+    }
+    Ok(())
+}
+
+/// True for errors that mean "this directory won't accept create/rename" even
+/// though the target file may be writable: `EROFS` (read-only fs) plus
+/// `EACCES`/`EPERM` (directory write denied).
+pub fn is_readonly_dir_error(e: &std::io::Error) -> bool {
+    if e.kind() == std::io::ErrorKind::PermissionDenied {
+        return true;
+    }
+    #[cfg(unix)]
+    {
+        matches!(
+            e.raw_os_error(),
+            Some(libc::EROFS | libc::EACCES | libc::EPERM)
+        )
+    }
+    #[cfg(not(unix))]
+    {
+        false
+    }
+}
+
+/// Atomic write with the read-only-directory in-place fallback. Tries the
+/// crash-atomic temp+rename first; if that fails because the *directory* is
+/// read-only/permission-denied but an existing file inode is writable, overwrite
+/// it in place. `permissions`, when given, is applied to the written file.
+pub fn write_bytes_with_fallback(
+    path: &Path,
+    bytes: &[u8],
+    permissions: Option<&std::fs::Permissions>,
+) -> Result<(), String> {
+    match try_atomic_write(path, bytes, permissions) {
+        Ok(()) => Ok(()),
+        Err(e) if is_readonly_dir_error(&e) && path.is_file() => {
+            in_place_overwrite(path, bytes, permissions).map_err(|fallback_err| {
+                format!(
+                    "atomic write failed ({e}); in-place fallback also failed: {fallback_err} ({})",
+                    path.display()
+                )
+            })
+        }
+        Err(e) => Err(format!("atomic write failed: {e} ({})", path.display())),
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn readonly_dir_error_classification() {
+        assert!(is_readonly_dir_error(&std::io::Error::from(
+            std::io::ErrorKind::PermissionDenied
+        )));
+        assert!(!is_readonly_dir_error(&std::io::Error::from(
+            std::io::ErrorKind::NotFound
+        )));
+        #[cfg(unix)]
+        {
+            assert!(is_readonly_dir_error(&std::io::Error::from_raw_os_error(
+                libc::EROFS
+            )));
+            assert!(is_readonly_dir_error(&std::io::Error::from_raw_os_error(
+                libc::EACCES
+            )));
+            assert!(is_readonly_dir_error(&std::io::Error::from_raw_os_error(
+                libc::EPERM
+            )));
+        }
+    }
+
+    #[test]
+    fn try_atomic_write_creates_and_replaces() {
+        let dir = tempfile::tempdir().unwrap();
+        let path = dir.path().join("cfg.toml");
+        try_atomic_write(&path, b"first", None).unwrap();
+        assert_eq!(std::fs::read(&path).unwrap(), b"first");
+        // No leftover temp files.
+        let strays: Vec<_> = std::fs::read_dir(dir.path())
+            .unwrap()
+            .flatten()
+            .filter(|e| e.file_name().to_string_lossy().contains(".agentflare.tmp."))
+            .collect();
+        assert!(strays.is_empty(), "temp file must not linger");
+        try_atomic_write(&path, b"second", None).unwrap();
+        assert_eq!(std::fs::read(&path).unwrap(), b"second");
+    }
+
+    #[cfg(unix)]
+    #[test]
+    fn try_atomic_write_preserves_existing_permissions_when_none_given() {
+        use std::os::unix::fs::PermissionsExt;
+        let dir = tempfile::tempdir().unwrap();
+        let path = dir.path().join("secret.json");
+        std::fs::write(&path, b"original").unwrap();
+        std::fs::set_permissions(&path, std::fs::Permissions::from_mode(0o600)).unwrap();
+
+        try_atomic_write(&path, b"updated", None).unwrap();
+
+        let mode = std::fs::metadata(&path).unwrap().permissions().mode() & 0o777;
+        assert_eq!(
+            mode, 0o600,
+            "replacement must keep the original file's mode"
+        );
+    }
+
+    #[cfg(unix)]
+    #[test]
+    fn try_atomic_write_writes_through_a_symlink() {
+        use std::os::unix::fs::symlink;
+        let dir = tempfile::tempdir().unwrap();
+        let real = dir.path().join("real.txt");
+        let link = dir.path().join("link.txt");
+        std::fs::write(&real, b"original").unwrap();
+        symlink(&real, &link).unwrap();
+
+        try_atomic_write(&link, b"updated", None).unwrap();
+
+        assert!(link.is_symlink(), "the symlink itself must survive");
+        assert_eq!(std::fs::read_link(&link).unwrap(), real);
+        assert_eq!(std::fs::read(&real).unwrap(), b"updated");
+    }
+
+    #[cfg(unix)]
+    #[test]
+    fn in_place_overwrite_truncates_existing_file() {
+        let dir = tempfile::tempdir().unwrap();
+        let path = dir.path().join("config.jsonc");
+        std::fs::write(&path, b"longer original content").unwrap();
+        in_place_overwrite(&path, b"short", None).unwrap();
+        assert_eq!(std::fs::read(&path).unwrap(), b"short");
+    }
+
+    #[cfg(unix)]
+    #[test]
+    fn fallback_overwrites_when_parent_dir_is_readonly() {
+        use std::os::unix::fs::PermissionsExt;
+        let dir = tempfile::tempdir().unwrap();
+        let path = dir.path().join("cfg.toml");
+        std::fs::write(&path, b"original").unwrap();
+        // Read-only parent dir: temp+rename is impossible, but the file inode
+        // stays writable, so the in-place fallback must succeed.
+        std::fs::set_permissions(dir.path(), std::fs::Permissions::from_mode(0o500)).unwrap();
+        let res = write_bytes_with_fallback(&path, b"updated", None);
+        let _ = std::fs::set_permissions(dir.path(), std::fs::Permissions::from_mode(0o700));
+        res.expect("read-only-dir fallback must succeed");
+        assert_eq!(std::fs::read(&path).unwrap(), b"updated");
+    }
+
+    #[test]
+    fn write_bytes_with_fallback_creates_new_file() {
+        let dir = tempfile::tempdir().unwrap();
+        let path = dir.path().join("new.txt");
+        write_bytes_with_fallback(&path, b"hello", None).unwrap();
+        assert_eq!(std::fs::read(&path).unwrap(), b"hello");
+    }
+}
diff --git a/src/auth.rs b/src/auth.rs
index 296c0aea..2ff8fbac 100644
--- a/src/auth.rs
+++ b/src/auth.rs
@@ -187,7 +187,8 @@ pub fn activate_with(agent: &str, profile: &str, reload_daemon: bool, json: bool
             if auth_crypt::is_encrypted(&data) {
                 if let Some(ref pw) = passphrase {
                     if let Some(decrypted) = auth_crypt::decrypt(&data, pw) {
-                        fs::write(&dest, decrypted).expect("write");
+                        crate::atomic_fs::write_bytes_with_fallback(&dest, &decrypted, None)
+                            .expect("write");
                     } else {
                         eprintln!(
                             "warning: cannot decrypt {} — wrong passphrase",
@@ -203,7 +204,7 @@ pub fn activate_with(agent: &str, profile: &str, reload_daemon: bool, json: bool
                     continue;
                 }
             } else {
-                fs::write(&dest, data).expect("write");
+                crate::atomic_fs::write_bytes_with_fallback(&dest, &data, None).expect("write");
             }
             restored += 1;
         }
@@ -1037,7 +1038,6 @@ fn read_isolate_mode(dir: &std::path::Path) -> Option<String> {
     }
     None
 }
-
 fn activate_into(agent: &str, profile: &str, target_dir: &std::path::Path) {
     let cat = match catalog_for(agent) {
         Some(c) => c,
@@ -1058,7 +1058,8 @@ fn activate_into(agent: &str, profile: &str, target_dir: &std::path::Path) {
             if auth_crypt::is_encrypted(&data) {
                 if let Some(ref pw) = passphrase {
                     if let Some(decrypted) = auth_crypt::decrypt(&data, pw) {
-                        fs::write(&dest, decrypted).expect("write");
+                        crate::atomic_fs::write_bytes_with_fallback(&dest, &decrypted, None)
+                            .expect("write");
                     } else {
                         eprintln!(
                             "warning: cannot decrypt {} — wrong passphrase",
@@ -1074,7 +1075,7 @@ fn activate_into(agent: &str, profile: &str, target_dir: &std::path::Path) {
                     continue;
                 }
             } else {
-                fs::write(&dest, data).expect("write");
+                crate::atomic_fs::write_bytes_with_fallback(&dest, &data, None).expect("write");
             }
         }
     }
diff --git a/src/main.rs b/src/main.rs
index 1387e37d..b19c6ff1 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -3,6 +3,7 @@ mod agent_launch;
 mod agents;
 mod alias;
 mod artifacts;
+mod atomic_fs;
 mod auth;
 mod auth_crypt;
 mod auth_db;