feat: AI tool rendering overhaul + edit_file tool (#3423)

Overhaul of how AI tool calls are modeled, rendered, and displayed in
the Atuin AI TUI. Fixes bugs in shell command output capture, implements
the `edit_file` tool with full safety infrastructure, and adds a diff
preview for edits.

1 files changed, 234 insertions, 0 deletions

diff --git a/crates/atuin-ai/src/file_tracker.rs b/crates/atuin-ai/src/file_tracker.rs
new file mode 100644
index 00000000..feee1ee8
--- /dev/null
+++ b/crates/atuin-ai/src/file_tracker.rs
@@ -0,0 +1,234 @@
+//! Tracks which files have been read in the current session, for freshness
+//! checking before edits.
+//!
+//! The tracker records the content hash and mtime of each file at the time
+//! it was last read. Before an edit, the tracker verifies the file hasn't
+//! changed since the last read — catching both external modifications and
+//! concurrent tool calls.
+//!
+//! Persisted as JSON in session metadata so it survives across CLI
+//! invocations within the same logical session.
+
+use std::collections::HashMap;
+use std::path::{Path, PathBuf};
+use std::time::SystemTime;
+
+use eyre::Result;
+use serde::{Deserialize, Serialize};
+
+/// Metadata key used for session_metadata persistence.
+pub(crate) const METADATA_KEY: &str = "file_read_tracker";
+
+/// State recorded for a single file read.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub(crate) struct FileReadState {
+    /// Hash of the file contents at the time of the last read.
+    pub content_hash: u64,
+    /// File mtime (as milliseconds since epoch) at the time of the last read.
+    /// Millisecond precision ensures sub-second modifications are detected.
+    pub mtime_ms: i64,
+}
+
+/// Tracks file read state for freshness checking.
+#[derive(Debug, Default, Clone, Serialize, Deserialize)]
+pub(crate) struct FileReadTracker {
+    reads: HashMap<PathBuf, FileReadState>,
+}
+
+/// Result of a freshness check.
+pub(crate) enum FreshnessCheck {
+    /// File is fresh — the content hasn't changed since the last read.
+    Fresh,
+    /// File has never been read in this session.
+    NotRead,
+    /// File has been modified since the last read.
+    Stale,
+}
+
+impl FileReadTracker {
+    /// Record that a file was read. Call this after a successful `read_file`
+    /// execution. The `path` should be canonical (absolute, tilde-expanded).
+    pub fn record_read(&mut self, path: PathBuf, content: &[u8], mtime: SystemTime) {
+        let content_hash = hash_content(content);
+        let mtime_ms = system_time_to_ms(mtime);
+
+        self.reads.insert(
+            path,
+            FileReadState {
+                content_hash,
+                mtime_ms,
+            },
+        );
+    }
+
+    /// Check whether a file is fresh (unchanged since last read).
+    ///
+    /// Uses mtime as a fast path — only re-hashes if mtime differs.
+    pub fn check_freshness(&self, path: &Path) -> Result<FreshnessCheck> {
+        let state = match self.reads.get(path) {
+            Some(s) => s,
+            None => return Ok(FreshnessCheck::NotRead),
+        };
+
+        // Stat the file
+        let metadata = match std::fs::metadata(path) {
+            Ok(m) => m,
+            Err(_) => return Ok(FreshnessCheck::Stale), // file deleted or inaccessible
+        };
+
+        let current_mtime_ms =
+            system_time_to_ms(metadata.modified().unwrap_or(SystemTime::UNIX_EPOCH));
+
+        // Fast path: mtime unchanged → fresh
+        if current_mtime_ms == state.mtime_ms {
+            return Ok(FreshnessCheck::Fresh);
+        }
+
+        // Mtime changed — re-hash to confirm
+        let content = std::fs::read(path)?;
+        let current_hash = hash_content(&content);
+
+        if current_hash == state.content_hash {
+            Ok(FreshnessCheck::Fresh)
+        } else {
+            Ok(FreshnessCheck::Stale)
+        }
+    }
+
+    /// Update the tracker entry after a successful edit (new content written).
+    pub fn update_after_edit(&mut self, path: &Path, new_content: &[u8], new_mtime: SystemTime) {
+        let content_hash = hash_content(new_content);
+        let mtime_ms = system_time_to_ms(new_mtime);
+
+        self.reads.insert(
+            path.to_path_buf(),
+            FileReadState {
+                content_hash,
+                mtime_ms,
+            },
+        );
+    }
+
+    /// Serialize to JSON for session metadata persistence.
+    pub fn to_json(&self) -> Result<String> {
+        Ok(serde_json::to_string(self)?)
+    }
+
+    /// Deserialize from JSON session metadata.
+    pub fn from_json(json: &str) -> Result<Self> {
+        Ok(serde_json::from_str(json)?)
+    }
+}
+
+fn system_time_to_ms(t: SystemTime) -> i64 {
+    t.duration_since(SystemTime::UNIX_EPOCH)
+        .map(|d| d.as_millis() as i64)
+        .unwrap_or(0)
+}
+
+fn hash_content(content: &[u8]) -> u64 {
+    xxhash_rust::xxh3::xxh3_64(content)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use std::io::Write;
+    use tempfile::NamedTempFile;
+
+    #[test]
+    fn record_and_check_fresh() {
+        let mut tracker = FileReadTracker::default();
+        let mut tmp = NamedTempFile::new().unwrap();
+        write!(tmp, "hello world").unwrap();
+
+        let path = tmp.path().to_path_buf();
+        let content = std::fs::read(&path).unwrap();
+        let mtime = std::fs::metadata(&path).unwrap().modified().unwrap();
+
+        tracker.record_read(path.clone(), &content, mtime);
+
+        assert!(matches!(
+            tracker.check_freshness(&path).unwrap(),
+            FreshnessCheck::Fresh
+        ));
+    }
+
+    #[test]
+    fn check_not_read() {
+        let tracker = FileReadTracker::default();
+        let path = PathBuf::from("/nonexistent/file.txt");
+        assert!(matches!(
+            tracker.check_freshness(&path).unwrap(),
+            FreshnessCheck::NotRead
+        ));
+    }
+
+    #[test]
+    fn check_stale_after_modification() {
+        let mut tracker = FileReadTracker::default();
+        let mut tmp = NamedTempFile::new().unwrap();
+        write!(tmp, "original").unwrap();
+
+        let path = tmp.path().to_path_buf();
+        let content = std::fs::read(&path).unwrap();
+        let mtime = std::fs::metadata(&path).unwrap().modified().unwrap();
+
+        tracker.record_read(path.clone(), &content, mtime);
+
+        // Small delay to ensure the filesystem mtime advances
+        std::thread::sleep(std::time::Duration::from_millis(10));
+
+        // Modify the file
+        std::fs::write(&path, "modified").unwrap();
+
+        assert!(matches!(
+            tracker.check_freshness(&path).unwrap(),
+            FreshnessCheck::Stale
+        ));
+    }
+
+    #[test]
+    fn update_after_edit_makes_fresh() {
+        let mut tracker = FileReadTracker::default();
+        let mut tmp = NamedTempFile::new().unwrap();
+        write!(tmp, "original").unwrap();
+
+        let path = tmp.path().to_path_buf();
+        let content = std::fs::read(&path).unwrap();
+        let mtime = std::fs::metadata(&path).unwrap().modified().unwrap();
+
+        tracker.record_read(path.clone(), &content, mtime);
+
+        // Simulate an edit
+        let new_content = b"edited content";
+        std::fs::write(&path, new_content).unwrap();
+        let new_mtime = std::fs::metadata(&path).unwrap().modified().unwrap();
+        tracker.update_after_edit(&path, new_content, new_mtime);
+
+        assert!(matches!(
+            tracker.check_freshness(&path).unwrap(),
+            FreshnessCheck::Fresh
+        ));
+    }
+
+    #[test]
+    fn roundtrip_json() {
+        let mut tracker = FileReadTracker::default();
+        tracker.reads.insert(
+            PathBuf::from("/some/file.toml"),
+            FileReadState {
+                content_hash: 12345,
+                mtime_ms: 1700000000000,
+            },
+        );
+
+        let json = tracker.to_json().unwrap();
+        let restored = FileReadTracker::from_json(&json).unwrap();
+        assert_eq!(restored.reads.len(), 1);
+        assert_eq!(
+            restored.reads[&PathBuf::from("/some/file.toml")].content_hash,
+            12345
+        );
+    }
+}