diff --git a/Cargo.lock b/Cargo.lock
index 7f09ee4..e972336 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -812,9 +812,9 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.5.13"
+version = "4.5.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0fbb260a053428790f3de475e304ff84cdbc4face759ea7a3e64c1edd938a7fc"
+checksum = "c937d4061031a6d0c8da4b9a4f98a172fc2976dfb1c19213a9cf7d0d3c837e36"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -822,9 +822,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.13"
+version = "4.5.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "64b17d7ea74e9f833c7dbf2cbe4fb12ff26783eda4782a8975b72f895c9b4d99"
+checksum = "85379ba512b21a328adf887e85f7742d12e96eb31f3ef077df4ffc26b506ffed"
 dependencies = [
  "anstream",
  "anstyle",
@@ -1374,14 +1374,14 @@ checksum = "9fc0510504f03c51ada170672ac806f1f105a88aa97a5281117e1ddc3368e51a"
 
 [[package]]
 name = "filetime"
-version = "0.2.23"
+version = "0.2.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1ee447700ac8aa0b2f2bd7bc4462ad686ba06baa6727ac149a2d6277f0d240fd"
+checksum = "bf401df4a4e3872c4fe8151134cf483738e74b67fc934d6532c882b3d24a4550"
 dependencies = [
  "cfg-if",
  "libc",
- "redox_syscall 0.4.1",
- "windows-sys 0.52.0",
+ "libredox",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
@@ -2382,8 +2382,7 @@ dependencies = [
 [[package]]
 name = "gix-worktree-state"
 version = "0.11.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "39ed6205b5f51067a485b11843babcf3304c0799e265a06eb0dde7f69cd85cd8"
+source = "git+https://github.com/daimond113/gitoxide?rev=753961c2cc23982a7d8c327dbc68c4dd26bce193#753961c2cc23982a7d8c327dbc68c4dd26bce193"
 dependencies = [
  "bstr",
  "gix-features",
@@ -2985,6 +2984,7 @@ checksum = "c0ff37bd590ca25063e35af745c343cb7a0271906fb7b37e4813e8f79f00268d"
 dependencies = [
  "bitflags 2.6.0",
  "libc",
+ "redox_syscall",
 ]
 
 [[package]]
@@ -3518,7 +3518,7 @@ checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
 dependencies = [
  "cfg-if",
  "libc",
- "redox_syscall 0.5.3",
+ "redox_syscall",
  "smallvec",
  "windows-targets 0.52.6",
 ]
@@ -3897,15 +3897,6 @@ dependencies = [
  "crossbeam-utils",
 ]
 
-[[package]]
-name = "redox_syscall"
-version = "0.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
-dependencies = [
- "bitflags 1.3.2",
-]
-
 [[package]]
 name = "redox_syscall"
 version = "0.5.3"
@@ -5209,9 +5200,9 @@ checksum = "8ecb6da28b8a351d773b68d5825ac39017e680750f980f3a1a85cd8dd28a47c1"
 
 [[package]]
 name = "ureq"
-version = "2.10.0"
+version = "2.10.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72139d247e5f97a3eff96229a7ae85ead5328a39efe76f8bf5a06313d505b6ea"
+checksum = "b74fc6b57825be3373f7054754755f03ac3a8f5d70015ccad699ba2029956f4a"
 dependencies = [
  "base64 0.22.1",
  "log",
@@ -5621,12 +5612,12 @@ dependencies = [
 
 [[package]]
 name = "xdg-home"
-version = "1.2.0"
+version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ca91dcf8f93db085f3a0a29358cd0b9d670915468f4290e8b85d118a34211ab8"
+checksum = "ec1cdab258fb55c0da61328dc52c8764709b249011b2cad0454c72f0bf10a1f6"
 dependencies = [
  "libc",
- "windows-sys 0.52.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
diff --git a/Cargo.toml b/Cargo.toml
index 8323537..5a9d3f3 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -82,6 +82,10 @@ indicatif = { version = "0.17.8", optional = true }
 indicatif-log-bridge = { version = "0.2.2", optional = true }
 inquire = { version = "0.7.5", optional = true }
 
+# TODO: remove this when a release with https://github.com/Byron/gitoxide/commit/aab78f102113330f96c3140c472aaab0912bc553 is available
+[patch.crates-io]
+gix-worktree-state = { git = "https://github.com/daimond113/gitoxide", rev = "753961c2cc23982a7d8c327dbc68c4dd26bce193" }
+
 [target.'cfg(target_os = "windows")'.dependencies]
 winreg = { version = "0.52.0", optional = true }
 
diff --git a/src/cli/scripts.rs b/src/cli/scripts.rs
index ca9e242..546712a 100644
--- a/src/cli/scripts.rs
+++ b/src/cli/scripts.rs
@@ -1,31 +1,94 @@
-use std::fs::remove_dir_all;
-
+use crate::{
+    cli::{config::read_config, home_dir},
+    util::authenticate_conn,
+};
 use anyhow::Context;
-
+use gix::remote::Direction;
 use pesde::Project;
 
-use crate::cli::{config::read_config, home_dir};
-
-pub fn update_scripts_folder(_project: &Project) -> anyhow::Result<()> {
+pub fn update_scripts_folder(project: &Project) -> anyhow::Result<()> {
     let scripts_dir = home_dir()?.join("scripts");
 
     if scripts_dir.exists() {
-        // checking out the repository seems to be corrupting the repository contents
-        // TODO: add actual `git pull`-esque functionality
-        remove_dir_all(&scripts_dir).context("failed to remove scripts directory")?;
-    }
+        let repo = gix::open(&scripts_dir).context("failed to open scripts repository")?;
 
-    std::fs::create_dir_all(&scripts_dir).context("failed to create scripts directory")?;
+        let remote = repo
+            .find_default_remote(Direction::Fetch)
+            .context("missing default remote of scripts repository")?
+            .context("failed to find default remote of scripts repository")?;
 
-    let cli_config = read_config()?;
+        let mut connection = remote
+            .connect(Direction::Fetch)
+            .context("failed to connect to default remote of scripts repository")?;
 
-    gix::prepare_clone(cli_config.scripts_repo, &scripts_dir)
-        .context("failed to prepare scripts repository clone")?
-        .fetch_then_checkout(gix::progress::Discard, &false.into())
-        .context("failed to fetch and checkout scripts repository")?
-        .0
-        .main_worktree(gix::progress::Discard, &false.into())
-        .context("failed to set scripts repository as main worktree")?;
+        authenticate_conn(&mut connection, project.auth_config());
+
+        let results = connection
+            .prepare_fetch(gix::progress::Discard, Default::default())
+            .context("failed to prepare scripts repository fetch")?
+            .receive(gix::progress::Discard, &false.into())
+            .context("failed to receive new scripts repository contents")?;
+
+        let remote_ref = results
+            .ref_map
+            .remote_refs
+            .first()
+            .context("failed to get remote refs of scripts repository")?;
+
+        let unpacked = remote_ref.unpack();
+        let oid = unpacked
+            .1
+            .or(unpacked.2)
+            .context("couldn't find oid in remote ref")?;
+
+        let tree = repo
+            .find_object(oid)
+            .context("failed to find scripts repository tree")?
+            .peel_to_tree()
+            .context("failed to peel scripts repository object to tree")?;
+
+        let mut index = gix::index::File::from_state(
+            gix::index::State::from_tree(&tree.id, &repo.objects, Default::default())
+                .context("failed to create index state from scripts repository tree")?,
+            repo.index_path(),
+        );
+
+        let opts = gix::worktree::state::checkout::Options {
+            overwrite_existing: true,
+            destination_is_initially_empty: false,
+            ..Default::default()
+        };
+
+        gix::worktree::state::checkout(
+            &mut index,
+            repo.work_dir().context("scripts repo is bare")?,
+            repo.objects
+                .clone()
+                .into_arc()
+                .context("failed to clone objects")?,
+            &gix::progress::Discard,
+            &gix::progress::Discard,
+            &false.into(),
+            opts,
+        )
+        .context("failed to checkout scripts repository")?;
+
+        index
+            .write(gix::index::write::Options::default())
+            .context("failed to write index")?;
+    } else {
+        std::fs::create_dir_all(&scripts_dir).context("failed to create scripts directory")?;
+
+        let cli_config = read_config()?;
+
+        gix::prepare_clone(cli_config.scripts_repo, &scripts_dir)
+            .context("failed to prepare scripts repository clone")?
+            .fetch_then_checkout(gix::progress::Discard, &false.into())
+            .context("failed to fetch and checkout scripts repository")?
+            .0
+            .main_worktree(gix::progress::Discard, &false.into())
+            .context("failed to set scripts repository as main worktree")?;
+    };
 
     Ok(())
 }
diff --git a/src/lib.rs b/src/lib.rs
index d6cf126..5b3aaee 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -155,7 +155,7 @@ impl Project {
     }
 }
 
-/// Errors that can occur when reading or writing files
+/// Errors that can occur when using the pesde library
 pub mod errors {
     use thiserror::Error;
 
diff --git a/src/main.rs b/src/main.rs
index 86c3374..96fb0d2 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -153,25 +153,6 @@ fn run() -> anyhow::Result<()> {
             .build()?
     };
 
-    match check_for_updates(&reqwest) {
-        Ok(_) => {}
-        Err(e) => {
-            println!(
-                "{}",
-                format!("failed to check for updates: {e}\n\n").red().bold()
-            );
-        }
-    }
-    match update_scripts_folder(&project) {
-        Ok(_) => {}
-        Err(e) => {
-            println!(
-                "{}",
-                format!("failed to update scripts: {e}\n\n").red().bold()
-            );
-        }
-    }
-
     let target_version = project
         .deser_manifest()
         .ok()
@@ -200,6 +181,26 @@ fn run() -> anyhow::Result<()> {
         std::process::exit(status.code().unwrap());
     }
 
+    match check_for_updates(&reqwest) {
+        Ok(_) => {}
+        Err(e) => {
+            println!(
+                "{}",
+                format!("failed to check for updates: {e}\n\n").red().bold()
+            );
+        }
+    }
+
+    match update_scripts_folder(&project) {
+        Ok(_) => {}
+        Err(e) => {
+            println!(
+                "{}",
+                format!("failed to update scripts: {e}\n\n").red().bold()
+            );
+        }
+    }
+
     Cli::parse().subcommand.run(project, multi, reqwest)
 }