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

README.md

@@ -38,6 +38,24 @@ sce doctor    # verify the install is healthy
 
 `sce setup` writes OpenCode, Claude Code, and/or Pi config into your repo, installs the required git hooks, and initializes the per-repo Agent Trace database. Use `sce setup --pi` for Pi only, or `sce setup --all` for OpenCode + Claude Code + Pi. `sce doctor` is read-only by default; `sce doctor --fix` will repair the issues it knows how to repair (missing or stale hooks, missing canonical DB parent directories) and report the rest for manual follow-up.
 
+With plain `sce setup`, after choosing targets and optional workflows, answer two independent confirmations:
+
+```text
+Enable automatic Agent Trace synchronization? [Y/n]
+Enable SCE commit attribution trailers? [Y/n]
+```
+
+Both default to Yes, so pressing Enter enables that choice; answering `n` disables only the corresponding behavior. A successful target setup persists the answers in `.sce/config.json`:
+
+```json
+{
+  "agent_trace": { "auto_sync": true },
+  "policies": { "attribution_hooks": { "enabled": true } }
+}
+```
+
+Non-interactive setup asks no questions. It explicitly enables both behaviors only when creating a missing repo-local config; an existing config's behavior values and omissions are not changed merely by a non-interactive run. Runtime precedence and hook behavior remain unchanged: `agent_trace.auto_sync` is config-file-only with omitted fallback `false`, while attribution can still be disabled by `SCE_ATTRIBUTION_HOOKS_DISABLED`, `SCE_DISABLED`, or its config value.
+
 ## Bash policy
 
 **Stop agents from running commands your repo does not allow.**

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,
@@ -564,7 +557,7 @@ where
             source: ValueSource::ConfigFile(value.source),
         },
         None => ResolvedValue {
-            value: true,
+            value: false,
             source: ValueSource::Default,
         },
     };
@@ -907,10 +900,10 @@ mod tests {
     }
 
     #[test]
-    fn agent_trace_auto_sync_defaults_to_true() {
+    fn agent_trace_auto_sync_defaults_to_false_when_missing() {
         let runtime = resolve_runtime_with_config(None).unwrap();
 
-        assert!(runtime.agent_trace_auto_sync.value);
+        assert!(!runtime.agent_trace_auto_sync.value);
         assert_eq!(runtime.agent_trace_auto_sync.source, ValueSource::Default);
     }
 

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
@@ -45,7 +44,14 @@ impl SetupCommand {
                 setup::SetupDispatch::Proceed {
                     mode: resolved_mode,
                     optional_workflows,
-                } => Some((resolved_mode, optional_workflows)),
+                    agent_trace_auto_sync,
+                    attribution_hooks_enabled,
+                } => Some((
+                    resolved_mode,
+                    optional_workflows,
+                    agent_trace_auto_sync,
+                    attribution_hooks_enabled,
+                )),
                 setup::SetupDispatch::Cancelled => {
                     return Ok(setup::setup_cancelled_text());
                 }
@@ -85,16 +91,27 @@ impl SetupCommand {
         }
 
         // Handle config target installation (OpenCode/Claude assets).
-        if let Some((resolved_mode, prompted_optional_workflows)) = setup_dispatch {
+        if let Some((
+            resolved_mode,
+            prompted_optional_workflows,
+            agent_trace_auto_sync,
+            attribution_hooks_enabled,
+        )) = setup_dispatch
+        {
             // A prompted selection is authoritative for the run; without one the
             // `--workflow` selection (or, absent that, the persisted one) applies.
             let optional_workflows = prompted_optional_workflows
                 .as_deref()
                 .or(self.request.optional_workflows.as_deref());
 
-            let setup_message =
-                setup::run_setup_for_mode(&repository_root, resolved_mode, optional_workflows)
-                    .map_err(CliError::runtime)?;
+            let setup_message = setup::run_setup_for_mode(
+                &repository_root,
+                resolved_mode,
+                optional_workflows,
+                agent_trace_auto_sync,
+                attribution_hooks_enabled,
+            )
+            .map_err(CliError::runtime)?;
             sections.push(setup_message);
         }
 

cli/src/services/setup/mod.rs

@@ -56,10 +56,11 @@ pub(crate) fn is_missing_git_remote_error(error: &anyhow::Error) -> bool {
 }
 
 /// Canonical JSON payload for a newly bootstrapped repo-local `.sce/config.json`.
-/// Contains only the `$schema` declaration pointing to the SCE config JSON Schema.
+/// Declares the SCE config JSON Schema and explicitly opts new repositories into
+/// Agent Trace post-commit synchronization.
 fn repo_local_config_bootstrap_payload() -> String {
     format!(
-        "{{\n  \"$schema\": \"{}\"\n}}\n",
+        "{{\n  \"$schema\": \"{}\",\n  \"agent_trace\": {{\n    \"auto_sync\": true\n  }},\n  \"policies\": {{\n    \"attribution_hooks\": {{\n      \"enabled\": true\n    }}\n  }}\n}}\n",
         crate::services::agent_trace::sce_config_schema_url()
     )
 }
@@ -229,6 +230,12 @@ pub enum SetupDispatch {
         /// The optional workflows this run installs. `None` means no selection
         /// was resolved here, so the persisted selection is reused downstream.
         optional_workflows: Option<Vec<String>>,
+        /// The interactive selection for automatic Agent Trace synchronization.
+        /// `None` means setup did not prompt for this value.
+        agent_trace_auto_sync: Option<bool>,
+        /// The interactive selection for SCE commit-attribution trailers.
+        /// `None` means setup did not prompt for this value.
+        attribution_hooks_enabled: Option<bool>,
     },
     Cancelled,
 }
@@ -400,6 +407,8 @@ pub fn run_setup_for_mode(
     repository_root: &Path,
     mode: SetupMode,
     optional_workflows: Option<&[String]>,
+    agent_trace_auto_sync: Option<bool>,
+    attribution_hooks_enabled: Option<bool>,
 ) -> Result<String> {
     let target = match mode {
         SetupMode::Interactive => {
@@ -425,13 +434,19 @@ pub fn run_setup_for_mode(
             })?;
 
     // Persist selected integration targets and optional workflows in repo-local config.
-    persist_integration_targets(repository_root, target, &selected_optional_workflows)
-        .with_context(|| {
-            format!(
-                "Setup assets were installed for {} but failed to update repo-local config",
-                setup_target_label(target)
-            )
-        })?;
+    persist_integration_targets(
+        repository_root,
+        target,
+        &selected_optional_workflows,
+        agent_trace_auto_sync,
+        attribution_hooks_enabled,
+    )
+    .with_context(|| {
+        format!(
+            "Setup assets were installed for {} but failed to update repo-local config",
+            setup_target_label(target)
+        )
+    })?;
 
     Ok(format_setup_install_success_message(&outcome))
 }
@@ -485,27 +500,11 @@ 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
-/// schema-only JSON payload. If the file already exists, it is left untouched.
+/// schema and explicit Agent Trace/attribution bootstrap JSON payload. If the
+/// file already exists, it is left untouched.
 pub fn bootstrap_repo_local_config(repository_root: &Path) -> Result<()> {
     let repo_paths = RepoPaths::new(repository_root);
     let config_file = repo_paths.sce_config_file();
@@ -841,10 +840,21 @@ pub fn persist_integration_targets(
     repository_root: &Path,
     target: SetupTarget,
     selected_optional_workflows: &[String],
+    agent_trace_auto_sync: Option<bool>,
+    attribution_hooks_enabled: Option<bool>,
 ) -> Result<()> {
     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)
@@ -901,6 +911,37 @@ pub fn persist_integration_targets(
         }),
     );
 
+    if let Some(value) = agent_trace_auto_sync {
+        let agent_trace = config_obj.entry("agent_trace").or_insert_with(|| json!({}));
+        let agent_trace_obj = agent_trace.as_object_mut().with_context(|| {
+            format!(
+                "Config file '{}' must contain an object at 'agent_trace'.",
+                config_file.display()
+            )
+        })?;
+        agent_trace_obj.insert("auto_sync".to_string(), json!(value));
+    }
+
+    if let Some(value) = attribution_hooks_enabled {
+        let policies = config_obj.entry("policies").or_insert_with(|| json!({}));
+        let policies_obj = policies.as_object_mut().with_context(|| {
+            format!(
+                "Config file '{}' must contain an object at 'policies'.",
+                config_file.display()
+            )
+        })?;
+        let attribution_hooks = policies_obj
+            .entry("attribution_hooks")
+            .or_insert_with(|| json!({}));
+        let attribution_hooks_obj = attribution_hooks.as_object_mut().with_context(|| {
+            format!(
+                "Config file '{}' must contain an object at 'policies.attribution_hooks'.",
+                config_file.display()
+            )
+        })?;
+        attribution_hooks_obj.insert("enabled".to_string(), json!(value));
+    }
+
     let updated = serde_json::to_string_pretty(&config).with_context(|| {
         format!(
             "Failed to serialize updated config for '{}'",
@@ -1617,6 +1658,14 @@ pub trait SetupTargetPrompter {
     /// The optional workflows to install, pre-checked from `defaults`.
     /// `None` means the operator cancelled the prompt.
     fn prompt_optional_workflows(&self, defaults: &[String]) -> Result<Option<Vec<String>>>;
+
+    /// Whether automatic Agent Trace synchronization should be enabled.
+    /// `None` means the operator cancelled the prompt.
+    fn prompt_agent_trace_auto_sync(&self) -> Result<Option<bool>>;
+
+    /// Whether SCE commit-attribution trailers should be enabled.
+    /// `None` means the operator cancelled the prompt.
+    fn prompt_attribution_hooks_enabled(&self) -> Result<Option<bool>>;
 }
 
 #[derive(Clone, Copy, Debug, Default)]
@@ -1630,6 +1679,14 @@ impl SetupTargetPrompter for InquireSetupTargetPrompter {
     fn prompt_optional_workflows(&self, defaults: &[String]) -> Result<Option<Vec<String>>> {
         prompt::prompt_optional_workflows(defaults)
     }
+
+    fn prompt_agent_trace_auto_sync(&self) -> Result<Option<bool>> {
+        prompt::prompt_agent_trace_auto_sync()
+    }
+
+    fn prompt_attribution_hooks_enabled(&self) -> Result<Option<bool>> {
+        prompt::prompt_attribution_hooks_enabled()
+    }
 }
 
 #[derive(Clone, Copy, Debug, Eq, PartialEq)]
@@ -1666,7 +1723,7 @@ fn setup_prompt_title_with_color_policy(color_enabled: bool) -> String {
 
 mod prompt {
     use anyhow::{bail, Result};
-    use inquire::{InquireError, MultiSelect, Select};
+    use inquire::{Confirm, InquireError, MultiSelect, Select};
 
     use crate::services::style::{
         prompt_label, prompt_label_with_color_policy, prompt_value_with_color_policy,
@@ -1678,6 +1735,8 @@ mod prompt {
         SetupDispatch::Proceed {
             mode: SetupMode::NonInteractive(target),
             optional_workflows: None,
+            agent_trace_auto_sync: None,
+            attribution_hooks_enabled: None,
         }
     }
 
@@ -1737,6 +1796,25 @@ mod prompt {
         }
     }
 
+    pub(super) fn prompt_agent_trace_auto_sync() -> Result<Option<bool>> {
+        prompt_confirmation("Enable automatic Agent Trace synchronization?")
+    }
+
+    pub(super) fn prompt_attribution_hooks_enabled() -> Result<Option<bool>> {
+        prompt_confirmation("Enable SCE commit attribution trailers?")
+    }
+
+    fn prompt_confirmation(label: &str) -> Result<Option<bool>> {
+        match Confirm::new(label).with_default(true).prompt() {
+            Ok(value) => Ok(Some(value)),
+            Err(InquireError::OperationCanceled | InquireError::OperationInterrupted) => Ok(None),
+            Err(InquireError::NotTTY) => bail!(
+                "Interactive setup requires a TTY. Re-run with '--non-interactive' and one of '--opencode', '--claude', '--pi', '--codex', or '--all'."
+            ),
+            Err(error) => Err(error.into()),
+        }
+    }
+
     /// One selectable row per optional workflow, in catalog order.
     #[derive(Clone, Copy, Debug, Eq, PartialEq)]
     pub(super) struct OptionalWorkflowRow {
@@ -1870,14 +1948,27 @@ where
                 return Ok(SetupDispatch::Cancelled);
             };
 
+            let Some(agent_trace_auto_sync) = prompter.prompt_agent_trace_auto_sync()? else {
+                return Ok(SetupDispatch::Cancelled);
+            };
+
+            let Some(attribution_hooks_enabled) = prompter.prompt_attribution_hooks_enabled()?
+            else {
+                return Ok(SetupDispatch::Cancelled);
+            };
+
             Ok(SetupDispatch::Proceed {
                 mode,
                 optional_workflows: Some(optional_workflows),
+                agent_trace_auto_sync: Some(agent_trace_auto_sync),
+                attribution_hooks_enabled: Some(attribution_hooks_enabled),
             })
         }
         SetupMode::NonInteractive(target) => Ok(SetupDispatch::Proceed {
             mode: SetupMode::NonInteractive(target),
             optional_workflows: None,
+            agent_trace_auto_sync: None,
+            attribution_hooks_enabled: None,
         }),
     }
 }
@@ -1956,7 +2047,7 @@ mod tests {
         assert_eq!(
             payload,
             format!(
-                "{{\n  \"$schema\": \"https://sce.crocoder.dev/v{}/config.json\"\n}}\n",
+                "{{\n  \"$schema\": \"https://sce.crocoder.dev/v{}/config.json\",\n  \"agent_trace\": {{\n    \"auto_sync\": true\n  }},\n  \"policies\": {{\n    \"attribution_hooks\": {{\n      \"enabled\": true\n    }}\n  }}\n}}\n",
                 env!("CARGO_PKG_VERSION")
             )
         );