diff --git a/lib/crates/fabro-cli/src/commands/graph.rs b/lib/crates/fabro-cli/src/commands/graph.rs
index cd8f9ee74..a8208bfe7 100644
--- a/lib/crates/fabro-cli/src/commands/graph.rs
+++ b/lib/crates/fabro-cli/src/commands/graph.rs
@@ -11,8 +11,7 @@ use std::io::Write;
 
 use anyhow::{Context, bail};
 use fabro_api::types;
-use fabro_config::user::{active_settings_path, load_settings_config};
-use fabro_types::settings::SettingsLayer;
+use fabro_config::user::active_settings_path;
 use fabro_util::terminal::Styles;
 use tracing::debug;
 
@@ -36,10 +35,9 @@ pub(crate) async fn run(
     let built = build_run_manifest(ManifestBuildInput {
         workflow:           args.workflow.clone(),
         cwd:                ctx.cwd().to_path_buf(),
-        args_layer:         SettingsLayer::default(),
+        args_layer:         Default::default(),
         args:               None,
         run_id:             None,
-        user_layer:         load_settings_config(None)?,
         user_settings_path: Some(active_settings_path(None)),
     })?;
     let client = ctx.server().await?;
diff --git a/lib/crates/fabro-cli/src/commands/parse.rs b/lib/crates/fabro-cli/src/commands/parse.rs
index 12088ca04..505671617 100644
--- a/lib/crates/fabro-cli/src/commands/parse.rs
+++ b/lib/crates/fabro-cli/src/commands/parse.rs
@@ -21,7 +21,7 @@ pub(crate) fn run(args: &ParseArgs) -> anyhow::Result<()> {
 }
 
 fn run_to(args: &ParseArgs, mut out: impl Write) -> anyhow::Result<()> {
-    let (dot_path, _cfg) = resolve_workflow(&args.workflow)?;
+    let dot_path = resolve_workflow(&args.workflow)?;
     let source = read_workflow_file(&dot_path)?;
     let ast = parse_ast(&source)?;
     serde_json::to_writer_pretty(&mut out, &ast)?;
diff --git a/lib/crates/fabro-cli/src/commands/preflight.rs b/lib/crates/fabro-cli/src/commands/preflight.rs
index 9cebf4f8c..0b6bdcbfe 100644
--- a/lib/crates/fabro-cli/src/commands/preflight.rs
+++ b/lib/crates/fabro-cli/src/commands/preflight.rs
@@ -1,5 +1,5 @@
 use anyhow::bail;
-use fabro_config::user::{active_settings_path, load_settings_config};
+use fabro_config::user::active_settings_path;
 use fabro_util::terminal::Styles;
 
 use crate::args::PreflightArgs;
@@ -26,7 +26,6 @@ pub(crate) async fn execute(
         args_layer:         preflight_args_layer(&args)?,
         args:               preflight_manifest_args(&args),
         run_id:             None,
-        user_layer:         load_settings_config(None)?,
         user_settings_path: Some(active_settings_path(None)),
     })?;
     let client = ctx.server().await?;
diff --git a/lib/crates/fabro-cli/src/commands/run/create.rs b/lib/crates/fabro-cli/src/commands/run/create.rs
index a2de07329..775ada9de 100644
--- a/lib/crates/fabro-cli/src/commands/run/create.rs
+++ b/lib/crates/fabro-cli/src/commands/run/create.rs
@@ -1,4 +1,4 @@
-use fabro_config::user::{active_settings_path, load_settings_config};
+use fabro_config::user::active_settings_path;
 use fabro_types::RunId;
 use fabro_util::terminal::Styles;
 
@@ -41,7 +41,6 @@ pub(crate) async fn create_run(
         args_layer: cli_args_config,
         args: run_manifest_args(args),
         run_id,
-        user_layer: load_settings_config(None)?,
         user_settings_path: Some(active_settings_path(None)),
     })?;
     let client = ctx.server().await?;
diff --git a/lib/crates/fabro-cli/src/commands/validate.rs b/lib/crates/fabro-cli/src/commands/validate.rs
index f174b1b73..19fcbc96a 100644
--- a/lib/crates/fabro-cli/src/commands/validate.rs
+++ b/lib/crates/fabro-cli/src/commands/validate.rs
@@ -1,6 +1,5 @@
 use anyhow::bail;
-use fabro_config::user::{active_settings_path, load_settings_config};
-use fabro_types::settings::SettingsLayer;
+use fabro_config::user::active_settings_path;
 use fabro_util::terminal::Styles;
 
 use crate::args::ValidateArgs;
@@ -19,10 +18,9 @@ pub(crate) async fn run(
     let built = build_run_manifest(ManifestBuildInput {
         workflow:           args.workflow.clone(),
         cwd:                ctx.cwd().to_path_buf(),
-        args_layer:         SettingsLayer::default(),
+        args_layer:         Default::default(),
         args:               None,
         run_id:             None,
-        user_layer:         load_settings_config(None)?,
         user_settings_path: Some(active_settings_path(None)),
     })?;
     let client = ctx.server().await?;
diff --git a/lib/crates/fabro-cli/src/commands/workflow/create.rs b/lib/crates/fabro-cli/src/commands/workflow/create.rs
index 742c3cad5..3a23280e5 100644
--- a/lib/crates/fabro-cli/src/commands/workflow/create.rs
+++ b/lib/crates/fabro-cli/src/commands/workflow/create.rs
@@ -16,14 +16,14 @@ pub(super) fn create_command(args: &WorkflowCreateArgs, base_ctx: &CommandContex
     let printer = base_ctx.printer();
     let cwd = std::env::current_dir()?;
 
-    let Some((config_path, config)) = discover_project_config(&cwd)? else {
+    let Some(config_path) = discover_project_config(&cwd)? else {
         bail!(
             "No .fabro/project.toml found in {cwd} or any parent directory",
             cwd = cwd.display()
         );
     };
 
-    let fabro_root = resolve_fabro_root(&config_path, &config);
+    let fabro_root = resolve_fabro_root(&config_path);
     let created = write_workflow_scaffold(args, &fabro_root)?;
 
     if base_ctx.json_output() {
diff --git a/lib/crates/fabro-cli/src/commands/workflow/list.rs b/lib/crates/fabro-cli/src/commands/workflow/list.rs
index 96553af73..16846762d 100644
--- a/lib/crates/fabro-cli/src/commands/workflow/list.rs
+++ b/lib/crates/fabro-cli/src/commands/workflow/list.rs
@@ -19,14 +19,14 @@ pub(super) fn list_command(_args: &WorkflowListArgs, base_ctx: &CommandContext)
     let styles = Styles::detect_stderr();
     let cwd = std::env::current_dir()?;
 
-    let Some((config_path, config)) = discover_project_config(&cwd)? else {
+    let Some(config_path) = discover_project_config(&cwd)? else {
         bail!(
             "No .fabro/project.toml found in {cwd} or any parent directory",
             cwd = cwd.display()
         );
     };
 
-    let fabro_root = resolve_fabro_root(&config_path, &config);
+    let fabro_root = resolve_fabro_root(&config_path);
     let project_wf_dir = fabro_root.join("workflows");
     let user_wf_dir = Some(fabro_util::Home::from_env().workflows_dir());
 
diff --git a/lib/crates/fabro-cli/src/manifest_builder.rs b/lib/crates/fabro-cli/src/manifest_builder.rs
index 3879d98bd..4f4d3ee59 100644
--- a/lib/crates/fabro-cli/src/manifest_builder.rs
+++ b/lib/crates/fabro-cli/src/manifest_builder.rs
@@ -28,9 +28,6 @@ pub(crate) struct ManifestBuildInput {
     pub args_layer:         SettingsLayer,
     pub args:               Option<types::ManifestArgs>,
     pub run_id:             Option<RunId>,
-    /// User-level settings layer. Production callers load via
-    /// `load_settings_config(None)`; tests pass `SettingsLayer::default()`.
-    pub user_layer:         SettingsLayer,
     /// Path to the user settings file (for inclusion in
     /// `RunManifest.configs`). `None` skips the user config entry.
     pub user_settings_path: Option<PathBuf>,
@@ -57,7 +54,7 @@ struct WorkflowScanInput {
 
 pub(crate) fn build_run_manifest(input: ManifestBuildInput) -> Result<BuiltManifest> {
     let root_resolution = resolve_workflow_path(&input.workflow, &input.cwd)?;
-    if root_resolution.workflow_config.is_none()
+    if root_resolution.workflow_toml_path.is_none()
         && !root_resolution.resolved_workflow_path.is_file()
     {
         return Err(fabro_config::Error::WorkflowNotFound(
@@ -70,16 +67,22 @@ pub(crate) fn build_run_manifest(input: ManifestBuildInput) -> Result<BuiltManif
         .parent()
         .unwrap_or_else(|| Path::new("."));
     let project_config = discover_project_config(workflow_parent)?;
-    let workflow_layer = root_resolution.workflow_config.clone().unwrap_or_default();
-    let project_layer = project_config
+    let mut workflow_settings_builder =
+        WorkflowSettingsBuilder::new().args_layer(input.args_layer.clone());
+    if let Some(path) = root_resolution.workflow_toml_path.as_ref() {
+        workflow_settings_builder = workflow_settings_builder.workflow_file(path)?;
+    }
+    if let Some(path) = project_config.as_ref() {
+        workflow_settings_builder = workflow_settings_builder.project_file(path)?;
+    }
+    if let Some(path) = input
+        .user_settings_path
         .as_ref()
-        .map(|(_, config)| config.clone())
-        .unwrap_or_default();
-    let workflow_settings = WorkflowSettingsBuilder::new()
-        .args_layer(input.args_layer.clone())
-        .workflow_layer(workflow_layer.clone())
-        .project_layer(project_layer)
-        .user_layer(input.user_layer.clone())
+        .filter(|path| path.is_file())
+    {
+        workflow_settings_builder = workflow_settings_builder.user_file(path)?;
+    }
+    let workflow_settings = workflow_settings_builder
         .build()
         .map_err(|errors| anyhow!("failed to resolve manifest settings: {errors}"))?;
     let target_path = root_resolution.dot_path.clone();
@@ -100,7 +103,7 @@ pub(crate) fn build_run_manifest(input: ManifestBuildInput) -> Result<BuiltManif
         .ok_or_else(|| anyhow!("root workflow missing from manifest bundle"))?;
 
     let mut configs = Vec::new();
-    if let Some((path, _config)) = project_config {
+    if let Some(path) = project_config {
         let source = std::fs::read_to_string(&path)
             .with_context(|| format!("Failed to read {}", path.display()))?;
         configs.push(types::ManifestConfig {
@@ -624,7 +627,6 @@ mod tests {
             args_layer:         SettingsLayer::default(),
             args:               None,
             run_id:             None,
-            user_layer:         SettingsLayer::default(),
             user_settings_path: None,
         })
         .unwrap();
@@ -704,7 +706,6 @@ file = "prompts/goal.md"
             args_layer:         SettingsLayer::default(),
             args:               None,
             run_id:             None,
-            user_layer:         SettingsLayer::default(),
             user_settings_path: None,
         })
         .unwrap();
@@ -757,7 +758,6 @@ file = "prompts/goal.md"
             args_layer:         SettingsLayer::default(),
             args:               None,
             run_id:             None,
-            user_layer:         SettingsLayer::default(),
             user_settings_path: None,
         })
         .unwrap();
diff --git a/lib/crates/fabro-config/src/builders.rs b/lib/crates/fabro-config/src/builders.rs
index 53e7e65a7..3f8d001b3 100644
--- a/lib/crates/fabro-config/src/builders.rs
+++ b/lib/crates/fabro-config/src/builders.rs
@@ -14,7 +14,7 @@ use crate::resolve::{
     resolve_workflow,
 };
 use crate::user::load_settings_config;
-use crate::{Error, Result};
+use crate::{Error, Result, run};
 
 #[derive(Debug, Clone, PartialEq, Eq)]
 pub struct ResolveErrors(pub Vec<ResolveError>);
@@ -186,18 +186,30 @@ impl WorkflowSettingsBuilder {
         self
     }
 
+    pub fn workflow_file(self, path: &Path) -> Result<Self> {
+        Ok(self.workflow_layer(run::load_run_config(path)?))
+    }
+
     #[must_use]
     pub fn project_layer(mut self, layer: SettingsLayer) -> Self {
         self.project = layer;
         self
     }
 
+    pub fn project_file(self, path: &Path) -> Result<Self> {
+        Ok(self.project_layer(load_settings_path(path)?))
+    }
+
     #[must_use]
     pub fn user_layer(mut self, layer: SettingsLayer) -> Self {
         self.user = layer;
         self
     }
 
+    pub fn user_file(self, path: &Path) -> Result<Self> {
+        Ok(self.user_layer(load_settings_path(path)?))
+    }
+
     #[must_use]
     pub fn server_layer(mut self, layer: SettingsLayer) -> Self {
         self.server = layer;
diff --git a/lib/crates/fabro-config/src/project.rs b/lib/crates/fabro-config/src/project.rs
index 4736db113..61239402c 100644
--- a/lib/crates/fabro-config/src/project.rs
+++ b/lib/crates/fabro-config/src/project.rs
@@ -23,7 +23,6 @@ const CONFIG_FILENAME: &str = ".fabro/project.toml";
 pub struct WorkflowPathResolution {
     pub resolved_workflow_path: PathBuf,
     pub dot_path:               PathBuf,
-    pub workflow_config:        Option<SettingsLayer>,
     pub workflow_toml_path:     Option<PathBuf>,
     pub workflow_slug:          Option<String>,
 }
@@ -32,7 +31,7 @@ pub struct WorkflowPathResolution {
 ///
 /// Goes through [`load_settings_path`] so that relative `run.goal.file`
 /// paths are anchored at the directory of `path` at load time.
-pub fn load_project_config(path: &Path) -> Result<SettingsLayer> {
+fn load_project_config(path: &Path) -> Result<SettingsLayer> {
     let config = load_settings_path(path)?;
     let root = WorkflowSettingsBuilder::project_from_layer(&config)
         .map_err(|errors| Error::resolve("Failed to resolve project settings", errors.into()))?
@@ -42,14 +41,13 @@ pub fn load_project_config(path: &Path) -> Result<SettingsLayer> {
 }
 
 /// Walk ancestor directories from `start` looking for `.fabro/project.toml`.
-/// Returns the config file path and parsed config, or `None` if not found.
-pub fn discover_project_config(start: &Path) -> Result<Option<(PathBuf, SettingsLayer)>> {
+/// Returns the config file path, or `None` if not found.
+pub fn discover_project_config(start: &Path) -> Result<Option<PathBuf>> {
     for ancestor in start.ancestors() {
         let candidate = ancestor.join(CONFIG_FILENAME);
         if candidate.is_file() {
             tracing::debug!(path = %candidate.display(), "Discovered project config");
-            let config = load_project_config(&candidate)?;
-            return Ok(Some((candidate, config)));
+            return Ok(Some(candidate));
         }
     }
     Ok(None)
@@ -93,7 +91,6 @@ pub fn resolve_workflow_path(workflow_path: &Path, cwd: &Path) -> Result<Workflo
                 Ok(WorkflowPathResolution {
                     resolved_workflow_path: path.clone(),
                     dot_path,
-                    workflow_config: Some(cfg),
                     workflow_toml_path: Some(path),
                     workflow_slug,
                 })
@@ -105,7 +102,6 @@ pub fn resolve_workflow_path(workflow_path: &Path, cwd: &Path) -> Result<Workflo
         Ok(WorkflowPathResolution {
             resolved_workflow_path: path.clone(),
             dot_path: path,
-            workflow_config: None,
             workflow_toml_path: None,
             workflow_slug,
         })
@@ -156,8 +152,8 @@ fn resolve_workflow_arg_impl(
 
     let name = arg.to_string_lossy();
     match discover_project_config(start_dir) {
-        Ok(Some((config_path, config))) => {
-            let fabro_root = resolve_fabro_root(&config_path, &config);
+        Ok(Some(config_path)) => {
+            let fabro_root = resolve_fabro_root(&config_path);
             let project_candidate = fabro_root
                 .join("workflows")
                 .join(&*name)
@@ -339,10 +335,10 @@ fn find_closest_match(input: &str, candidates: &[String]) -> Option<String> {
 }
 
 /// Resolve a workflow argument to a DOT path and optional run config.
-pub fn resolve_workflow(arg: &Path) -> Result<(PathBuf, Option<SettingsLayer>)> {
+pub fn resolve_workflow(arg: &Path) -> Result<PathBuf> {
     let start = std::env::current_dir().unwrap_or_else(|_| PathBuf::from("."));
     let resolution = resolve_workflow_path(arg, &start)?;
-    Ok((resolution.dot_path, resolution.workflow_config))
+    Ok(resolution.dot_path)
 }
 
 /// Check whether retros are enabled in the project config.
@@ -350,11 +346,15 @@ pub fn resolve_workflow(arg: &Path) -> Result<(PathBuf, Option<SettingsLayer>)>
 pub fn is_retro_enabled() -> bool {
     let start = std::env::current_dir().unwrap_or_else(|_| PathBuf::from("."));
     match discover_project_config(&start) {
-        Ok(Some((_path, config))) => config
-            .run
-            .as_ref()
-            .and_then(|r| r.execution.as_ref())
-            .and_then(|e| e.retros)
+        Ok(Some(path)) => load_project_config(&path)
+            .ok()
+            .and_then(|config| {
+                config
+                    .run
+                    .as_ref()
+                    .and_then(|r| r.execution.as_ref())
+                    .and_then(|e| e.retros)
+            })
             .unwrap_or(false),
         _ => false,
     }
@@ -383,11 +383,12 @@ fn normalize_joined_path(base_dir: &Path, reference: &Path) -> PathBuf {
 /// Resolve the fabro root directory from a config file path and its config.
 /// The returned path is the config file's parent directory joined with the
 /// `project.directory` value (default: `.`).
-pub fn resolve_fabro_root(config_path: &Path, config: &SettingsLayer) -> PathBuf {
+pub fn resolve_fabro_root(config_path: &Path) -> PathBuf {
     let project_dir = config_path
         .parent()
         .expect("config_path should have a parent directory");
-    let root = WorkflowSettingsBuilder::project_from_layer(config)
+    let config = load_project_config(config_path).expect("project config should load");
+    let root = WorkflowSettingsBuilder::project_from_layer(&config)
         .expect("project settings should resolve")
         .directory;
     normalize_joined_path(project_dir, Path::new(&root))
@@ -488,9 +489,8 @@ retros = true
         let sub = tmp.path().join("sub").join("dir");
         fs::create_dir_all(&sub).unwrap();
 
-        let (found_path, config) = discover_project_config(&sub).unwrap().unwrap();
+        let found_path = discover_project_config(&sub).unwrap().unwrap();
         assert_eq!(found_path, config_dir.join("project.toml"));
-        assert_eq!(config.version, Some(1));
     }
 
     #[test]
@@ -529,9 +529,7 @@ file = "prompts/goal.md"
         let config_path = config_dir.join("project.toml");
         fs::write(&config_path, "_version = 1\n").unwrap();
 
-        let config = load_project_config(&config_path).unwrap();
-
-        assert_eq!(resolve_fabro_root(&config_path, &config), config_dir);
+        assert_eq!(resolve_fabro_root(&config_path), config_dir);
     }
 
     #[test]
@@ -550,12 +548,7 @@ directory = "../custom"
         )
         .unwrap();
 
-        let config = load_project_config(&config_path).unwrap();
-
-        assert_eq!(
-            resolve_fabro_root(&config_path, &config),
-            tmp.path().join("custom")
-        );
+        assert_eq!(resolve_fabro_root(&config_path), tmp.path().join("custom"));
     }
 
     #[test]