fix(assistant): avoid recreating BOOTSTRAP.md after bootstrap completion

src/apps/desktop/src/lib.rs

@@ -141,6 +141,7 @@ pub async fn run() {
                 .level_for("tracing", log::LevelFilter::Off)
                 .level_for("opentelemetry_sdk", log::LevelFilter::Off)
                 .level_for("opentelemetry-otlp", log::LevelFilter::Off)
+                .level_for("notify", log::LevelFilter::Off)
                 .level_for("hyper_util", log::LevelFilter::Info)
                 .level_for("h2", log::LevelFilter::Info)
                 .level_for("portable_pty", log::LevelFilter::Info)

src/crates/core/src/agentic/coordination/coordinator.rs

@@ -18,7 +18,7 @@ use crate::agentic::session::SessionManager;
 use crate::agentic::tools::pipeline::{SubagentParentInfo, ToolPipeline};
 use crate::agentic::WorkspaceBinding;
 use crate::service::bootstrap::{
-    initialize_workspace_persona_files, is_workspace_bootstrap_pending,
+    ensure_workspace_persona_files_for_prompt, is_workspace_bootstrap_pending,
 };
 use crate::util::errors::{BitFunError, BitFunResult};
 use log::{debug, error, info, warn};
@@ -743,8 +743,8 @@ Update the persona files and delete BOOTSTRAP.md as soon as bootstrap is complet
     ) -> BitFunResult<AssistantBootstrapEnsureOutcome> {
         let workspace_root = PathBuf::from(&workspace_path);
         // Empty or partial assistant dirs may never have run create_assistant_workspace; fill only
-        // missing persona stubs (never overwrite). Ensures BOOTSTRAP.md exists when appropriate.
-        initialize_workspace_persona_files(&workspace_root).await?;
+        // missing persona stubs (never overwrite), while preserving completed bootstrap state.
+        ensure_workspace_persona_files_for_prompt(&workspace_root).await?;
         let bootstrap_pending = is_workspace_bootstrap_pending(&workspace_root);
         if !bootstrap_pending {
             return Ok(AssistantBootstrapEnsureOutcome::Skipped {

src/crates/core/src/service/bootstrap/bootstrap.rs

@@ -237,8 +237,9 @@ fn persona_file_description(file_name: &str) -> &'static str {
 #[cfg(test)]
 mod tests {
     use super::{
-        initialize_workspace_persona_files, normalize_line_endings, BOOTSTRAP_FILE_NAME,
-        IDENTITY_FILE_NAME, SOUL_FILE_NAME, USER_FILE_NAME,
+        ensure_workspace_persona_files_for_prompt, initialize_workspace_persona_files,
+        normalize_line_endings, BOOTSTRAP_FILE_NAME, IDENTITY_FILE_NAME, SOUL_FILE_NAME,
+        USER_FILE_NAME,
     };
     use std::time::{SystemTime, UNIX_EPOCH};
     use tokio::fs;
@@ -288,4 +289,45 @@ mod tests {
             .await
             .expect("Failed to remove temp workspace");
     }
+
+    #[tokio::test]
+    async fn ensure_workspace_persona_files_for_prompt_preserves_completed_bootstrap() {
+        let unique = SystemTime::now()
+            .duration_since(UNIX_EPOCH)
+            .expect("System time before unix epoch")
+            .as_nanos();
+        let workspace_root = std::env::temp_dir().join(format!(
+            "bitfun-bootstrap-preserve-{}-{}",
+            std::process::id(),
+            unique
+        ));
+
+        fs::create_dir_all(&workspace_root)
+            .await
+            .expect("Failed to create temp workspace");
+
+        fs::write(workspace_root.join(USER_FILE_NAME), "user")
+            .await
+            .expect("Failed to write USER.md");
+        fs::write(workspace_root.join(IDENTITY_FILE_NAME), "identity")
+            .await
+            .expect("Failed to write IDENTITY.md");
+
+        ensure_workspace_persona_files_for_prompt(&workspace_root)
+            .await
+            .expect("Failed to ensure persona files for prompt");
+
+        assert!(
+            !workspace_root.join(BOOTSTRAP_FILE_NAME).exists(),
+            "BOOTSTRAP.md should not be recreated when USER.md and IDENTITY.md already exist"
+        );
+        assert!(
+            workspace_root.join(SOUL_FILE_NAME).exists(),
+            "SOUL.md should still be backfilled"
+        );
+
+        fs::remove_dir_all(&workspace_root)
+            .await
+            .expect("Failed to remove temp workspace");
+    }
 }

src/crates/core/src/service/bootstrap/mod.rs

@@ -2,6 +2,7 @@ mod bootstrap;
 
 pub use bootstrap::reset_workspace_persona_files_to_default;
 pub(crate) use bootstrap::{
-    build_workspace_persona_prompt, initialize_workspace_persona_files,
+    build_workspace_persona_prompt, ensure_workspace_persona_files_for_prompt,
+    initialize_workspace_persona_files,
     is_workspace_bootstrap_pending,
 };