Fix: Allow Setup and Agent Trace to Degrade on Invalid Discovered Config

cli/src/services/config/resolver.rs

@@ -187,13 +187,6 @@ where
         resolve_global_config_path,
     )?;
 
-    if !runtime.validation_errors.is_empty() {
-        bail!(
-            "Agent Trace storage config resolution failed because a discovered config file is invalid: {}",
-            runtime.validation_errors.join(" | ")
-        );
-    }
-
     Ok(ResolvedAgentTraceStorageRuntimeConfig {
         repository_id: runtime.agent_trace_repository_id.value,
         repository_remote: runtime.agent_trace_repository_remote.value,

cli/src/services/setup/command.rs

@@ -23,7 +23,6 @@ impl SetupCommand {
         // The repository root is resolved before any prompt so the interactive
         // optional-workflow prompt can pre-check the persisted selection.
         let repository_root = resolve_setup_repository(&setup_start_path)?;
-        setup::validate_existing_repo_local_config(&repository_root).map_err(CliError::runtime)?;
 
         let setup_dispatch = if self.request.context_only {
             None

cli/src/services/setup/mod.rs

@@ -485,23 +485,6 @@ pub fn ensure_git_remote(repository_root: &Path, remote_name: &str) -> Result<()
     }))
 }
 
-/// Validates an existing repo-local `.sce/config.json` before setup performs
-/// any other repository or lifecycle work. An absent config remains eligible
-/// for the normal bootstrap path.
-pub fn validate_existing_repo_local_config(repository_root: &Path) -> Result<()> {
-    let config_file = RepoPaths::new(repository_root).sce_config_file();
-    if !config_file.exists() {
-        return Ok(());
-    }
-
-    crate::services::config::validate_config_file(&config_file).with_context(|| {
-        format!(
-            "Setup preflight rejected invalid repo-local config file '{}'",
-            config_file.display()
-        )
-    })
-}
-
 /// Bootstraps the repo-local `.sce/config.json` file if it does not already exist.
 ///
 /// Creates the `.sce/` parent directory as needed, then writes the canonical
@@ -845,6 +828,15 @@ pub fn persist_integration_targets(
     let repo_paths = RepoPaths::new(repository_root);
     let config_file = repo_paths.sce_config_file();
 
+    // Default-discovered invalid config is intentionally degradable during
+    // setup. Do not rewrite it while recording the installed target: the
+    // startup resolver already reported the invalid layer and setup must leave
+    // the user's file byte-for-byte unchanged.
+    if config_file.exists() && crate::services::config::validate_config_file(&config_file).is_err()
+    {
+        return Ok(());
+    }
+
     // Read existing config or start with bootstrap payload.
     let raw = if config_file.exists() {
         fs::read_to_string(&config_file)