diff --git a/src/cli/commands/cas/prune.rs b/src/cli/commands/cas/prune.rs
index 7410531..448cd0b 100644
--- a/src/cli/commands/cas/prune.rs
+++ b/src/cli/commands/cas/prune.rs
@@ -1,13 +1,38 @@
+use crate::cli::{
+	reporters::run_with_reporter,
+	style::{INFO_STYLE, SUCCESS_STYLE},
+};
 use anyhow::Context;
+use async_stream::try_stream;
 use clap::Args;
 use fs_err::tokio as fs;
-use pesde::Project;
-use std::{collections::HashSet, path::Path};
+use futures::{future::BoxFuture, FutureExt, Stream, StreamExt};
+use pesde::{
+	source::fs::{FsEntry, PackageFs},
+	Project,
+};
+use std::{
+	collections::{HashMap, HashSet},
+	future::Future,
+	path::{Path, PathBuf},
+};
 use tokio::task::JoinSet;
 
 #[derive(Debug, Args)]
 pub struct PruneCommand {}
 
+async fn read_dir_stream(
+	dir: &Path,
+) -> std::io::Result<impl Stream<Item = std::io::Result<fs::DirEntry>>> {
+	let mut read_dir = fs::read_dir(dir).await?;
+
+	Ok(try_stream! {
+		while let Some(entry) = read_dir.next_entry().await? {
+			yield entry;
+		}
+	})
+}
+
 #[allow(unreachable_code)]
 async fn get_nlinks(path: &Path) -> anyhow::Result<u64> {
 	#[cfg(unix)]
@@ -67,64 +92,138 @@ async fn get_nlinks(path: &Path) -> anyhow::Result<u64> {
 	anyhow::bail!("unsupported platform")
 }
 
-async fn remove_hashes(cas_dir: &Path) -> anyhow::Result<HashSet<String>> {
-	let mut tasks = JoinSet::new();
+#[derive(Debug)]
+struct ExtendJoinSet<T: Send + 'static>(JoinSet<T>);
 
-	let mut cas_entries = fs::read_dir(cas_dir)
-		.await
-		.context("failed to read directory")?;
-
-	while let Some(cas_entry) = cas_entries
-		.next_entry()
-		.await
-		.context("failed to read dir entry")?
-	{
-		let prefix = cas_entry.file_name();
-		let Some(prefix) = prefix.to_str() else {
-			continue;
-		};
-		// we only want hash directories
-		if prefix.len() != 2 {
-			continue;
+impl<T: Send + 'static, F: Future<Output = T> + Send + 'static> Extend<F> for ExtendJoinSet<T> {
+	fn extend<I: IntoIterator<Item = F>>(&mut self, iter: I) {
+		for item in iter {
+			self.0.spawn(item);
 		}
+	}
+}
 
-		let prefix = prefix.to_string();
+impl<T: Send + 'static> Default for ExtendJoinSet<T> {
+	fn default() -> Self {
+		Self(JoinSet::new())
+	}
+}
 
-		tasks.spawn(async move {
-			let mut hash_entries = fs::read_dir(cas_entry.path())
+async fn discover_cas_packages(cas_dir: &Path) -> anyhow::Result<HashMap<PathBuf, PackageFs>> {
+	fn read_entry(
+		entry: fs::DirEntry,
+	) -> BoxFuture<'static, anyhow::Result<HashMap<PathBuf, PackageFs>>> {
+		async move {
+			if entry
+				.metadata()
 				.await
-				.context("failed to read hash directory")?;
-
-			let mut tasks = JoinSet::new();
-
-			while let Some(hash_entry) = hash_entries
-				.next_entry()
-				.await
-				.context("failed to read hash dir entry")?
+				.context("failed to read entry metadata")?
+				.is_dir()
 			{
-				let hash = hash_entry.file_name();
-				let hash = hash.to_str().expect("non-UTF-8 hash").to_string();
-				let hash = format!("{prefix}{hash}");
+				let mut tasks = read_dir_stream(&entry.path())
+					.await
+					.context("failed to read entry directory")?
+					.map(|entry| async move {
+						read_entry(entry.context("failed to read inner cas index dir entry")?).await
+					})
+					.collect::<ExtendJoinSet<Result<_, anyhow::Error>>>()
+					.await
+					.0;
 
-				let path = hash_entry.path();
-				tasks.spawn(async move {
-					let nlinks = get_nlinks(&path)
-						.await
-						.context("failed to count file usage")?;
-					if nlinks != 1 {
-						return Ok::<_, anyhow::Error>(None);
-					}
+				let mut res = HashMap::new();
+				while let Some(entry) = tasks.join_next().await {
+					res.extend(entry.unwrap()?);
+				}
 
-					fs::remove_file(path)
-						.await
-						.context("failed to remove unused file")?;
+				return Ok(res);
+			};
 
-					Ok::<_, anyhow::Error>(Some(hash))
-				});
+			let contents = fs::read_to_string(entry.path()).await?;
+			let fs = toml::from_str(&contents).context("failed to deserialize PackageFs")?;
+
+			Ok(HashMap::from([(entry.path(), fs)]))
+		}
+		.boxed()
+	}
+
+	let mut tasks = ["index", "wally_index", "git_index"]
+		.into_iter()
+		.map(|index| cas_dir.join(index))
+		.map(|index| async move {
+			let mut tasks = read_dir_stream(&index)
+				.await
+				.context("failed to read index directory")?
+				.map(|entry| async move {
+					read_entry(entry.context("failed to read cas index dir entry")?).await
+				})
+				.collect::<ExtendJoinSet<Result<_, anyhow::Error>>>()
+				.await
+				.0;
+
+			let mut res = HashMap::new();
+
+			while let Some(task) = tasks.join_next().await {
+				res.extend(task.unwrap()?);
 			}
 
-			let mut removed_hashes = HashSet::new();
+			Ok(res)
+		})
+		.collect::<JoinSet<Result<_, anyhow::Error>>>();
 
+	let mut cas_entries = HashMap::new();
+
+	while let Some(task) = tasks.join_next().await {
+		cas_entries.extend(task.unwrap()?);
+	}
+
+	Ok(cas_entries)
+}
+
+async fn remove_hashes(cas_dir: &Path) -> anyhow::Result<HashSet<String>> {
+	let mut tasks = read_dir_stream(cas_dir)
+		.await?
+		.map(|cas_entry| async move {
+			let cas_entry = cas_entry.context("failed to read cas dir entry")?;
+			let prefix = cas_entry.file_name();
+			let Some(prefix) = prefix.to_str() else {
+				return Ok(None);
+			};
+			// we only want hash directories
+			if prefix.len() != 2 {
+				return Ok(None);
+			}
+
+			let mut tasks = read_dir_stream(&cas_entry.path())
+				.await
+				.context("failed to read hash directory")?
+				.map(|hash_entry| {
+					let prefix = prefix.to_string();
+					async move {
+						let hash_entry = hash_entry.context("failed to read hash dir entry")?;
+						let hash = hash_entry.file_name();
+						let hash = hash.to_str().expect("non-UTF-8 hash").to_string();
+						let hash = format!("{prefix}{hash}");
+
+						let path = hash_entry.path();
+						let nlinks = get_nlinks(&path)
+							.await
+							.context("failed to count file usage")?;
+						if nlinks > 1 {
+							return Ok(None);
+						}
+
+						fs::remove_file(path)
+							.await
+							.context("failed to remove unused file")?;
+
+						Ok(Some(hash))
+					}
+				})
+				.collect::<ExtendJoinSet<Result<_, anyhow::Error>>>()
+				.await
+				.0;
+
+			let mut removed_hashes = HashSet::new();
 			while let Some(removed_hash) = tasks.join_next().await {
 				let Some(hash) = removed_hash.unwrap()? else {
 					continue;
@@ -133,14 +232,20 @@ async fn remove_hashes(cas_dir: &Path) -> anyhow::Result<HashSet<String>> {
 				removed_hashes.insert(hash);
 			}
 
-			Ok::<_, anyhow::Error>(removed_hashes)
-		});
-	}
+			Ok(Some(removed_hashes))
+		})
+		.collect::<ExtendJoinSet<Result<_, anyhow::Error>>>()
+		.await
+		.0;
 
 	let mut res = HashSet::new();
 
 	while let Some(removed_hashes) = tasks.join_next().await {
-		res.extend(removed_hashes.unwrap()?);
+		let Some(removed_hashes) = removed_hashes.unwrap()? else {
+			continue;
+		};
+
+		res.extend(removed_hashes);
 	}
 
 	Ok(res)
@@ -154,8 +259,58 @@ impl PruneCommand {
 		// /wally_index/hash/name/version
 		// /git_index/hash/hash
 		// the last thing in the path is the serialized PackageFs
-		let _ = remove_hashes(project.cas_dir()).await?;
 
-		todo!("remove unused index entries");
+		let (cas_entries, removed_hashes) = run_with_reporter(|_, root_progress, _| async {
+			let root_progress = root_progress;
+			root_progress.reset();
+			root_progress.set_message("discover packages");
+			let cas_entries = discover_cas_packages(project.cas_dir()).await?;
+			root_progress.reset();
+			root_progress.set_message("remove unused files");
+			let removed_hashes = remove_hashes(project.cas_dir()).await?;
+
+			Ok::<_, anyhow::Error>((cas_entries, removed_hashes))
+		})
+		.await?;
+
+		let mut tasks = JoinSet::new();
+
+		let mut removed_packages = 0usize;
+
+		'entry: for (path, fs) in cas_entries {
+			let PackageFs::CAS(entries) = fs else {
+				continue;
+			};
+
+			for entry in entries.into_values() {
+				let FsEntry::File(hash) = entry else {
+					continue;
+				};
+
+				if removed_hashes.contains(&hash) {
+					tasks.spawn(async move {
+						fs::remove_file(path)
+							.await
+							.context("failed to remove unused file")
+					});
+					removed_packages += 1;
+					// if at least one file is removed, the package is not used
+					continue 'entry;
+				}
+			}
+		}
+
+		while let Some(task) = tasks.join_next().await {
+			task.unwrap()?;
+		}
+
+		println!(
+			"{} removed {} unused packages and {} individual files!",
+			SUCCESS_STYLE.apply_to("done!"),
+			INFO_STYLE.apply_to(removed_packages),
+			INFO_STYLE.apply_to(removed_hashes.len())
+		);
+
+		Ok(())
 	}
 }