diff --git a/crates/pile-config/src/lib.rs b/crates/pile-config/src/lib.rs
index 4012d06..d25936b 100644
--- a/crates/pile-config/src/lib.rs
+++ b/crates/pile-config/src/lib.rs
@@ -33,9 +33,6 @@ pub struct DatasetConfig {
 	/// Must be unique
 	pub name: Label,
 
-	/// Root dir for indices
-	pub working_dir: Option<PathBuf>,
-
 	/// Where to find this field
 	pub source: HashMap<Label, Source>,
 }
diff --git a/crates/pile-dataset/src/dataset.rs b/crates/pile-dataset/src/dataset.rs
index da56f0c..0ba2855 100644
--- a/crates/pile-dataset/src/dataset.rs
+++ b/crates/pile-dataset/src/dataset.rs
@@ -102,8 +102,6 @@ impl Datasets {
 		let config = ConfigToml {
 			dataset: DatasetConfig {
 				name: Label::new("virtual-dataset").unwrap(),
-				working_dir: None,
-
 				source: [(
 					Self::virt_source(),
 					Source::Filesystem {
@@ -155,7 +153,10 @@ impl Datasets {
 		});
 	}
 
-	pub async fn open(config: impl Into<PathBuf>) -> Result<Self, std::io::Error> {
+	pub async fn open(
+		config: impl Into<PathBuf>,
+		working_dir_root: impl Into<PathBuf>,
+	) -> Result<Self, std::io::Error> {
 		let path_config = config.into();
 		let path_parent = path_config
 			.parent()
@@ -184,12 +185,7 @@ impl Datasets {
 			}
 		};
 
-		let path_workdir = config
-			.dataset
-			.working_dir
-			.clone()
-			.unwrap_or(path_parent.join(".pile"))
-			.join(config.dataset.name.as_str());
+		let path_workdir = working_dir_root.into().join(config.dataset.name.as_str());
 
 		let mut sources = HashMap::new();
 		let mut disabled_sources = HashMap::new();
diff --git a/crates/pile/src/command/check.rs b/crates/pile/src/command/check.rs
index 6d71d9f..033d760 100644
--- a/crates/pile/src/command/check.rs
+++ b/crates/pile/src/command/check.rs
@@ -13,6 +13,10 @@ pub struct CheckCommand {
 	/// Path to dataset config
 	#[arg(long, short = 'c', default_value = "./pile.toml")]
 	config: PathBuf,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for CheckCommand {
@@ -43,7 +47,7 @@ impl CliCmd for CheckCommand {
 			}
 		}
 
-		let ds = Datasets::open(&self.config)
+		let ds = Datasets::open(&self.config, self.workdir)
 			.await
 			.with_context(|| format!("while opening dataset for {}", self.config.display()))?;
 
diff --git a/crates/pile/src/command/fields.rs b/crates/pile/src/command/fields.rs
index 3ff61d0..b1596a0 100644
--- a/crates/pile/src/command/fields.rs
+++ b/crates/pile/src/command/fields.rs
@@ -43,6 +43,10 @@ pub struct FieldsCommand {
 	/// Restrict to these sources (all sources if empty)
 	#[arg(long, short = 's')]
 	source: Vec<String>,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for FieldsCommand {
@@ -53,7 +57,7 @@ impl CliCmd for FieldsCommand {
 		_ctx: GlobalContext,
 		flag: CancelFlag,
 	) -> Result<i32, CancelableTaskError<anyhow::Error>> {
-		let ds = Datasets::open(&self.config)
+		let ds = Datasets::open(&self.config, &self.workdir)
 			.await
 			.with_context(|| format!("while opening dataset for {}", self.config.display()))?;
 
diff --git a/crates/pile/src/command/index.rs b/crates/pile/src/command/index.rs
index 9e53070..c7d751c 100644
--- a/crates/pile/src/command/index.rs
+++ b/crates/pile/src/command/index.rs
@@ -16,6 +16,10 @@ pub struct IndexCommand {
 	/// Number of threads to use for indexing
 	#[arg(long, short = 'j', default_value = "3")]
 	jobs: usize,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for IndexCommand {
@@ -24,7 +28,7 @@ impl CliCmd for IndexCommand {
 		_ctx: GlobalContext,
 		flag: CancelFlag,
 	) -> Result<i32, CancelableTaskError<anyhow::Error>> {
-		let ds = Datasets::open(&self.config)
+		let ds = Datasets::open(&self.config, &self.workdir)
 			.await
 			.with_context(|| format!("while opening dataset for {}", self.config.display()))?;
 
diff --git a/crates/pile/src/command/item.rs b/crates/pile/src/command/item.rs
index 5d40910..17e1e1a 100644
--- a/crates/pile/src/command/item.rs
+++ b/crates/pile/src/command/item.rs
@@ -30,6 +30,10 @@ pub struct ItemCommand {
 	/// Path to dataset config
 	#[arg(long, short = 'c', default_value = "./pile.toml")]
 	config: PathBuf,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for ItemCommand {
@@ -43,7 +47,7 @@ impl CliCmd for ItemCommand {
 		let source = Label::new(&self.source)
 			.ok_or_else(|| anyhow::anyhow!("invalid source name {:?}", self.source))?;
 
-		let ds = Datasets::open(&self.config)
+		let ds = Datasets::open(&self.config, &self.workdir)
 			.await
 			.with_context(|| format!("while opening dataset for {}", self.config.display()))?;
 
diff --git a/crates/pile/src/command/list.rs b/crates/pile/src/command/list.rs
index b2943a1..8087eac 100644
--- a/crates/pile/src/command/list.rs
+++ b/crates/pile/src/command/list.rs
@@ -31,6 +31,10 @@ pub struct ListCommand {
 	/// Restrict to these sources (all sources if empty)
 	#[arg(long, short = 's')]
 	source: Vec<String>,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for ListCommand {
@@ -44,7 +48,7 @@ impl CliCmd for ListCommand {
 			.with_context(|| format!("invalid path {:?}", self.path))?;
 		let path = Arc::new(path);
 
-		let ds = Datasets::open(&self.config)
+		let ds = Datasets::open(&self.config, &self.workdir)
 			.await
 			.with_context(|| format!("while opening dataset for {}", self.config.display()))?;
 
diff --git a/crates/pile/src/command/lookup.rs b/crates/pile/src/command/lookup.rs
index e2e341a..ea08a9f 100644
--- a/crates/pile/src/command/lookup.rs
+++ b/crates/pile/src/command/lookup.rs
@@ -31,6 +31,10 @@ pub struct LookupCommand {
 	/// Number of threads to use for indexing
 	#[arg(long, short = 'j', default_value = "3")]
 	jobs: usize,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for LookupCommand {
@@ -40,7 +44,7 @@ impl CliCmd for LookupCommand {
 		_ctx: GlobalContext,
 		flag: CancelFlag,
 	) -> Result<i32, CancelableTaskError<anyhow::Error>> {
-		let ds = Datasets::open(&self.config)
+		let ds = Datasets::open(&self.config, &self.workdir)
 			.await
 			.with_context(|| format!("while opening dataset for {}", self.config.display()))?;
 
diff --git a/crates/pile/src/command/serve.rs b/crates/pile/src/command/serve.rs
index 4c14c92..df4462f 100644
--- a/crates/pile/src/command/serve.rs
+++ b/crates/pile/src/command/serve.rs
@@ -25,6 +25,10 @@ pub struct ServeCommand {
 	/// Number of threads to use for indexing
 	#[arg(long, short = 'j', default_value = "3")]
 	jobs: usize,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for ServeCommand {
@@ -33,7 +37,7 @@ impl CliCmd for ServeCommand {
 		_ctx: GlobalContext,
 		flag: CancelFlag,
 	) -> Result<i32, CancelableTaskError<anyhow::Error>> {
-		let ds = Datasets::open(&self.config)
+		let ds = Datasets::open(&self.config, &self.workdir)
 			.await
 			.with_context(|| format!("while opening dataset for {}", self.config.display()))?;
 
diff --git a/crates/pile/src/command/server.rs b/crates/pile/src/command/server.rs
index 6754acd..80a0a15 100644
--- a/crates/pile/src/command/server.rs
+++ b/crates/pile/src/command/server.rs
@@ -35,6 +35,10 @@ pub struct ServerCommand {
 	/// If provided, require this bearer token for all requests
 	#[arg(long)]
 	token: Option<String>,
+
+	/// Working directory root
+	#[arg(long, default_value = "./.pile")]
+	workdir: PathBuf,
 }
 
 impl CliCmd for ServerCommand {
@@ -46,7 +50,7 @@ impl CliCmd for ServerCommand {
 		let datasets = {
 			let mut datasets = Vec::new();
 			for c in &self.config {
-				let ds = Datasets::open(&c)
+				let ds = Datasets::open(&c, &self.workdir)
 					.await
 					.with_context(|| format!("while opening dataset for {}", c.display()))?;
 				datasets.push(Arc::new(ds));