diff --git a/crates/nao/src/lib.rs b/crates/nao/src/lib.rs
index 4aeb876c5d..9b443fe10a 100644
--- a/crates/nao/src/lib.rs
+++ b/crates/nao/src/lib.rs
@@ -312,9 +312,12 @@ impl Nao {
     ) -> Result<()> {
         let mut command = self.rsync_with_nao(true)?;
         command
-            .arg("--keep-dirlinks")
+            .arg("--copy-dirlinks")
             .arg("--copy-links")
             .arg("--info=progress2")
+            .arg("--exclude=.git")
+            .arg("--exclude=webots")
+            .arg("--filter=dir-merge,- .gitignore")
             .arg(format!("{}/", local_directory.as_ref().display()))
             .arg(format!(
                 "{}:{}/",
diff --git a/crates/repository/src/upload.rs b/crates/repository/src/upload.rs
index 5fa0ac9d94..04591bd1f8 100644
--- a/crates/repository/src/upload.rs
+++ b/crates/repository/src/upload.rs
@@ -1,13 +1,7 @@
-use std::{ffi::OsString, path::Path};
+use std::path::Path;
 
-use color_eyre::{
-    eyre::{bail, Context},
-    Result,
-};
-use tokio::{
-    fs::{create_dir_all, symlink},
-    process::Command,
-};
+use color_eyre::{eyre::Context, Result};
+use tokio::fs::{create_dir_all, symlink};
 
 pub async fn populate_upload_directory(
     upload_directory: impl AsRef<Path>,
@@ -31,28 +25,9 @@ pub async fn populate_upload_directory(
     .await
     .wrap_err("failed to link executable")?;
 
-    create_dir_all(upload_directory.join("logs"))
+    symlink(repository_root, upload_directory.join("source"))
         .await
-        .wrap_err("failed to create directory for logs")?;
-
-    let source_file = upload_directory.join("logs/source.tar.gz");
-
-    let mut archive_command = OsString::from("cd ");
-    archive_command.push(repository_root);
-    archive_command.push(" && git ls-files --cached --others --exclude-standard | tar Tczf - ");
-    archive_command.push(source_file);
-
-    let mut command = Command::new("sh");
-    command.arg("-c").arg(archive_command);
-
-    let status = command
-        .status()
-        .await
-        .wrap_err("failed to run archive command")?;
-
-    if !status.success() {
-        bail!("archive command failed with {status}")
-    }
+        .wrap_err("failed to link source directory")?;
 
     Ok(())
 }
diff --git a/tools/pepsi/src/upload.rs b/tools/pepsi/src/upload.rs
index 503623e57b..8906f5906e 100644
--- a/tools/pepsi/src/upload.rs
+++ b/tools/pepsi/src/upload.rs
@@ -65,7 +65,7 @@ async fn upload_with_progress(
             .get_os_version()
             .await
             .wrap_err_with(|| format!("failed to get OS version of {nao_address}"))?;
-        let expected_os_version = read_os_version(repository_root)
+        let expected_os_version = read_os_version(&repository_root)
             .await
             .wrap_err("failed to get configured OS version")?;
         if nao_os_version != expected_os_version {