upgrade gix to the latest release 0.69. (#14975)

The main benefit is that it won't facilitate hangs due to attempts to
read from untrackable directory entries, like names pipes or sockets.

Related to GitoxideLabs/gitoxide#1629

### Tasks

* [x] upgrade
* [x] incorporate updated `gix` [once everything is
fixed](GitoxideLabs/gitoxide#1740).
* [x] assure tests work

### Postponed

It turns out that the new `gix` version doesn't magically fix the FIFO
issue, so the following test still fails.

It's not super-trivial to fix apparently (I tried), so let's do it in a
separate PR.

Here is the patch I have so far in case anyone is interested to fix it
earlier or wants to share insights :).

```patch
commit dfef545eae215f0b9da9f3d4424b52cba7edaec3
Author: Sebastian Thiel <[email protected]>
Date:   Sun Dec 22 19:05:40 2024 +0100

    fix: assure possibly blocking non-files (like FIFOs) won't be picked up for publishing.

    This would otherwise cause the publish to hang.

diff --git a/src/cargo/sources/path.rs b/src/cargo/sources/path.rs
index 776590697..c78463a32 100644
--- a/src/cargo/sources/path.rs
+++ b/src/cargo/sources/path.rs
@@ -626,8 +626,11 @@ fn list_files_gix(
         .filter(|res| {
             // Don't include Cargo.lock if it is untracked. Packaging will
             // generate a new one as needed.
+            // Also don't include untrackable directory entries, like FIFOs.
             res.as_ref().map_or(true, |item| {
-                !(item.entry.status == Status::Untracked && item.entry.rela_path == "Cargo.lock")
+                item.entry.disk_kind != Some(gix::dir::entry::Kind::Untrackable)
+                    && !(item.entry.status == Status::Untracked
+                        && item.entry.rela_path == "Cargo.lock")
             })
         })
         .map(|res| res.map(|item| (item.entry.rela_path, item.entry.disk_kind)))
diff --git a/tests/testsuite/package.rs b/tests/testsuite/package.rs
index 1740de4ac..1c6b3db89 100644
--- a/tests/testsuite/package.rs
+++ b/tests/testsuite/package.rs
@@ -6873,3 +6873,29 @@ See https://doc.rust-lang.org/cargo/reference/manifest.html#package-metadata for
 "#]])
         .run();
 }
+
+#[cargo_test]
+#[cfg(unix)]
+fn simple_with_fifo() {
+    let p = project()
+        .file(
+            "Cargo.toml",
+            r#"
+                [package]
+                name = "foo"
+                version = "0.1.0"
+                edition = "2015"
+            "#,
+        )
+        .file("src/main.rs", "fn main() {}")
+        .build();
+
+    std::process::Command::new("mkfifo")
+        .current_dir(p.root())
+        .arg(p.root().join("blocks-when-read"))
+        .status()
+        .expect("a FIFO can be created");
+
+    // If this hangs, Cargo tried to package a FIFO and is reading it forever.
+    p.cargo("package").run();
+}
```

Author: weihanglo

Cargo.lock

@@ -49,7 +49,7 @@ filetime = "0.2.23"
 flate2 = { version = "1.0.30", default-features = false, features = ["zlib"] }
 git2 = "0.19.0"
 git2-curl = "0.20.0"
-gix = { version = "0.68.0", default-features = false, features = ["blocking-http-transport-curl", "progress-tree", "parallel", "dirwalk"] }
+gix = { version = "0.69.1", default-features = false, features = ["blocking-http-transport-curl", "progress-tree", "parallel", "dirwalk"] }
 glob = "0.3.1"
 handlebars = { version = "6.0.0", features = ["dir_source"] }
 hex = "0.4.3"

Cargo.toml

@@ -352,7 +352,7 @@ pub fn cargo_config_to_gitoxide_overrides(gctx: &GlobalContext) -> CargoResult<V
 }
 
 /// Reinitializes a given Git repository. This is useful when a Git repository
-/// seems corrupted and we want to start over.
+/// seems corrupted, and we want to start over.
 pub fn reinitialize(git_dir: &Path) -> CargoResult<()> {
     fn init(path: &Path, bare: bool) -> CargoResult<()> {
         let mut opts = git2::RepositoryInitOptions::new();

src/cargo/sources/git/oxide.rs

@@ -1057,7 +1057,9 @@ pub fn fetch(
 fn has_shallow_lock_file(err: &crate::sources::git::fetch::Error) -> bool {
     matches!(
         err,
-        gix::env::collate::fetch::Error::Fetch(gix::remote::fetch::Error::LockShallowFile(_))
+        gix::env::collate::fetch::Error::Fetch(gix::remote::fetch::Error::Fetch(
+            gix::protocol::fetch::Error::LockShallowFile(_)
+        ))
     )
 }