trim config wrapper and storage override helpers

lib/crates/fabro-cli/src/command_context.rs

@@ -187,9 +187,9 @@ mod tests {
     use std::path::PathBuf;
 
     use fabro_config::parse_settings_layer;
-    use fabro_config::user::apply_storage_dir_override;
     use fabro_types::settings::InterpString;
     use fabro_types::settings::cli::{CliLayer, CliOutputLayer, OutputFormat, OutputVerbosity};
+    use fabro_types::settings::server::{ServerLayer, ServerStorageLayer};
     use fabro_util::printer::Printer;
     use tokio::sync::OnceCell;
 
@@ -223,6 +223,18 @@ mod tests {
         }
     }
 
+    fn with_storage_dir_override(
+        mut layer: fabro_types::settings::SettingsLayer,
+        path: &std::path::Path,
+    ) -> fabro_types::settings::SettingsLayer {
+        let server = layer.server.get_or_insert_with(ServerLayer::default);
+        let storage = server
+            .storage
+            .get_or_insert_with(ServerStorageLayer::default);
+        storage.root = Some(InterpString::parse(&path.display().to_string()));
+        layer
+    }
+
     #[test]
     fn context_exposes_resolved_output_and_explicit_json_state() {
         let ctx = synthetic_context(true, Printer::Default);
@@ -248,9 +260,9 @@ root = "/srv/fabro/default"
 "#,
         )
         .expect("settings fixture should parse");
-        let override_disk_settings = apply_storage_dir_override(
+        let override_disk_settings = with_storage_dir_override(
             base_disk_settings.clone(),
-            Some(std::path::Path::new("/srv/fabro/override")),
+            std::path::Path::new("/srv/fabro/override"),
         );
 
         let (base_settings, base_user_settings) =

lib/crates/fabro-cli/src/commands/install.rs

@@ -1464,16 +1464,13 @@ async fn run_install_github_inner(
 
     let existing_config_contents =
         std::fs::read_to_string(&config_path).context("failed to read existing settings.toml")?;
-    let parsed_settings = user_config::apply_storage_dir_override(
-        fabro_config::parse_settings_layer(&existing_config_contents)
-            .context("failed to parse existing settings.toml")?,
-        args.storage_dir.as_deref(),
-    );
-    let storage_dir = local_server::storage_dir(&parsed_settings).unwrap_or_else(|_| {
-        args.storage_dir
-            .clone_path()
-            .unwrap_or_else(default_storage_dir)
-    });
+    let parsed_settings = fabro_config::parse_settings_layer(&existing_config_contents)
+        .context("failed to parse existing settings.toml")?;
+    let storage_dir = args
+        .storage_dir
+        .clone_path()
+        .or_else(|| local_server::storage_dir(&parsed_settings).ok())
+        .unwrap_or_else(default_storage_dir);
     let server_was_running =
         ServerDaemon::load_running(&Storage::new(&storage_dir).runtime_directory())?.is_some();
     let mut doc: toml::Value = toml::from_str(&existing_config_contents)
@@ -1777,11 +1774,8 @@ async fn run_install_inner(args: &InstallArgs, ctx: &CommandContext) -> Result<(
         toml::to_string_pretty(&doc)?
     };
 
-    let install_settings = user_config::apply_storage_dir_override(
-        fabro_config::parse_settings_layer(&settings_toml)
-            .context("failed to parse generated settings.toml")?,
-        args.storage_dir.as_deref(),
-    );
+    let install_settings = fabro_config::parse_settings_layer(&settings_toml)
+        .context("failed to parse generated settings.toml")?;
     fabro_config::ServerSettingsBuilder::from_layer(&install_settings)?;
 
     // Secrets and auth material

lib/crates/fabro-cli/src/manifest_builder.rs

@@ -9,8 +9,9 @@ use std::path::{Component, Path, PathBuf};
 use anyhow::{Context, Result, anyhow};
 use fabro_api::types;
 use fabro_config::load::load_settings_for_workflow;
+use fabro_config::parse_settings_layer;
 use fabro_config::project::{self, discover_project_config, resolve_workflow_path};
-use fabro_config::run::{parse_run_config, resolve_run_goal};
+use fabro_config::run::resolve_run_goal;
 use fabro_graphviz::graph::AttrValue;
 use fabro_graphviz::parser;
 use fabro_sandbox::daytona::detect_repo_info;
@@ -325,7 +326,8 @@ fn collect_workflow_config_files(
     config: &types::ManifestWorkflowConfig,
     files: &mut HashMap<String, types::ManifestFileEntry>,
 ) -> Result<()> {
-    let config_layer = parse_run_config(&config.source)?;
+    let config_layer = parse_settings_layer(&config.source)
+        .map_err(|err| anyhow!("Failed to parse run config TOML: {err}"))?;
     let dockerfile = config_layer
         .run
         .as_ref()

lib/crates/fabro-cli/src/user_config.rs

@@ -4,7 +4,8 @@ use std::str::FromStr;
 use anyhow::Result;
 pub(crate) use fabro_client::ServerTarget;
 use fabro_config::UserSettingsBuilder;
-pub(crate) use fabro_config::user::*;
+pub(crate) use fabro_config::user::{active_settings_path, default_storage_dir};
+use fabro_config::user::{default_socket_path, load_settings_config};
 use fabro_types::settings::cli::CliTargetSettings;
 use fabro_types::settings::{CliNamespace, SettingsLayer};
 use fabro_util::version::FABRO_VERSION;
@@ -31,6 +32,24 @@ pub(crate) fn load_settings_with_config_and_storage_dir(
     Ok(apply_storage_dir_override(layer, storage_dir))
 }
 
+fn apply_storage_dir_override(
+    mut layer: SettingsLayer,
+    storage_dir: Option<&Path>,
+) -> SettingsLayer {
+    use fabro_types::settings::InterpString;
+    use fabro_types::settings::server::{ServerLayer, ServerStorageLayer};
+
+    if let Some(dir) = storage_dir {
+        let server = layer.server.get_or_insert_with(ServerLayer::default);
+        let storage = server
+            .storage
+            .get_or_insert_with(ServerStorageLayer::default);
+        storage.root = Some(InterpString::parse(&dir.display().to_string()));
+    }
+
+    layer
+}
+
 /// Pull the resolved CLI target configuration out of `[cli.target]`.
 /// Returns either an http(s) URL or a unix socket path.
 fn cli_target_from_settings(settings: &CliNamespace) -> Option<String> {

lib/crates/fabro-config/src/run.rs

@@ -1,9 +1,8 @@
 //! Workflow / run config loading helpers.
 //!
-//! Thin wrappers around `parse_settings_layer` / `load_settings_path` plus
-//! path resolution for the `[workflow] graph` override. Runtime types
-//! that used to be re-exported from here live under
-//! `fabro_types::settings::run` now.
+//! Helpers for loading workflow-local settings and resolving runtime goal /
+//! graph paths. Runtime types that used to be re-exported from here live
+//! under `fabro_types::settings::run` now.
 
 #![expect(
     clippy::disallowed_methods,
@@ -15,15 +14,8 @@ use std::path::{Path, PathBuf};
 use fabro_types::settings::SettingsLayer;
 use fabro_types::settings::run::{ResolvedGoalSource, ResolvedRunGoal, RunGoalLayer};
 
+use crate::Result;
 use crate::load::{load_settings_path, resolve_goal_file_path};
-use crate::parse::parse_settings_layer;
-use crate::{Error, Result};
-
-/// Load and parse a run config from a TOML file.
-pub fn parse_run_config(contents: &str) -> Result<SettingsLayer> {
-    parse_settings_layer(contents)
-        .map_err(|err| Error::parse("Failed to parse run config TOML", err))
-}
 
 /// Load and parse a run config from a TOML file.
 ///

lib/crates/fabro-config/src/user.rs

@@ -63,24 +63,6 @@ fn load_v2_layer_from_path(path: &Path) -> Result<SettingsLayer> {
     load_settings_path(path)
 }
 
-/// Override the resolved storage root in a settings layer with a runtime path.
-pub fn apply_storage_dir_override(
-    mut layer: SettingsLayer,
-    storage_dir: Option<&Path>,
-) -> SettingsLayer {
-    use fabro_types::settings::interp::InterpString;
-    use fabro_types::settings::server::{ServerLayer, ServerStorageLayer};
-    if let Some(dir) = storage_dir {
-        let server = layer.server.get_or_insert_with(ServerLayer::default);
-        let storage = server
-            .storage
-            .get_or_insert_with(ServerStorageLayer::default);
-        storage.root = Some(InterpString::parse(&dir.display().to_string()));
-    }
-
-    layer
-}
-
 #[cfg(test)]
 mod tests {
     use super::{

lib/crates/fabro-server/src/run_manifest.rs

@@ -5,7 +5,6 @@ use std::sync::Arc;
 use anyhow::{Result, anyhow, bail};
 use fabro_api::types;
 use fabro_config::project::resolve_working_directory;
-use fabro_config::run::parse_run_config;
 use fabro_config::{WorkflowSettingsBuilder, parse_settings_layer};
 use fabro_graphviz::graph::{Graph, is_llm_handler_type};
 use fabro_graphviz::render::apply_direction;
@@ -199,7 +198,8 @@ fn root_workflow_config_layer(
         return Ok(SettingsLayer::default());
     };
 
-    let mut layer = parse_run_config(&config.source)?;
+    let mut layer = parse_settings_layer(&config.source)
+        .map_err(|err| anyhow!("Failed to parse run config TOML: {err}"))?;
     resolve_manifest_dockerfile(&mut layer, Path::new(&config.path), &workflow.files)?;
     Ok(layer)
 }

lib/crates/fabro-server/src/serve.rs

@@ -6,12 +6,12 @@ use std::time::Duration;
 use anyhow::Context;
 use clap::Args;
 use fabro_config::bind::{self, Bind, BindRequest};
-use fabro_config::user::{apply_storage_dir_override, load_settings_config};
+use fabro_config::user::load_settings_config;
 use fabro_config::{ServerSettingsBuilder, Storage};
 use fabro_install::{OBJECT_STORE_ACCESS_KEY_ID_ENV, OBJECT_STORE_SECRET_ACCESS_KEY_ENV};
 use fabro_sandbox::SandboxProvider;
 use fabro_types::settings::server::{
-    GithubIntegrationStrategy, ServerLayer, ServerListenLayer, WebhookStrategy,
+    GithubIntegrationStrategy, ServerLayer, ServerListenLayer, ServerStorageLayer, WebhookStrategy,
 };
 use fabro_types::settings::{
     Combine, GithubIntegrationSettings, InterpString, ObjectStoreSettings, ServerListenSettings,
@@ -191,7 +191,16 @@ fn apply_runtime_settings(
     args: &ServeArgs,
     data_dir: &Path,
 ) -> SettingsLayer {
-    apply_storage_dir_override(apply_serve_overrides(base, args), Some(data_dir))
+    apply_storage_dir_override(apply_serve_overrides(base, args), data_dir)
+}
+
+fn apply_storage_dir_override(mut settings: SettingsLayer, data_dir: &Path) -> SettingsLayer {
+    let server = settings.server.get_or_insert_with(ServerLayer::default);
+    let storage = server
+        .storage
+        .get_or_insert_with(ServerStorageLayer::default);
+    storage.root = Some(InterpString::parse(&data_dir.display().to_string()));
+    settings
 }
 
 async fn resolve_github_webhook_ip_allowlist(