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 https://github.com/GitoxideLabs/gitoxide/pull/1629

### Tasks

* [x] upgrade
* [x] incorporate updated `gix` [once everything is
fixed](https://github.com/GitoxideLabs/gitoxide/pull/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 <sebastian.thiel@icloud.com>
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();
+}
```

Cargo.lock

@@ -1161,9 +1161,9 @@ dependencies = [
 
 [[package]]
 name = "gix"
-version = "0.68.0"
+version = "0.69.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b04c66359b5e17f92395abc433861df0edf48f39f3f590818d1d7217327dd6a1"
+checksum = "8d0eebdaecdcf405d5433a36f85e4f058cf4de48ee2604388be0dbccbaad353e"
 dependencies = [
  "gix-actor",
  "gix-attributes",
@@ -1197,6 +1197,7 @@ dependencies = [
  "gix-revision",
  "gix-revwalk",
  "gix-sec",
+ "gix-shallow",
  "gix-submodule",
  "gix-tempfile",
  "gix-trace",
@@ -1263,9 +1264,9 @@ dependencies = [
 
 [[package]]
 name = "gix-command"
-version = "0.3.11"
+version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6d7d6b8f3a64453fd7e8191eb80b351eb7ac0839b40a1237cd2c137d5079fe53"
+checksum = "9405c0a56e17f8365a46870cd2c7db71323ecc8bda04b50cb746ea37bd091e90"
 dependencies = [
  "bstr",
  "gix-path",
@@ -1323,9 +1324,9 @@ dependencies = [
 
 [[package]]
 name = "gix-credentials"
-version = "0.25.1"
+version = "0.26.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2be87bb8685fc7e6e7032ef71c45068ffff609724a0c897b8047fde10db6ae71"
+checksum = "82a50c56b785c29a151ab4ccf74a83fe4e21d2feda0d30549504b4baed353e0a"
 dependencies = [
  "bstr",
  "gix-command",
@@ -1340,9 +1341,9 @@ dependencies = [
 
 [[package]]
 name = "gix-date"
-version = "0.9.2"
+version = "0.9.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "691142b1a34d18e8ed6e6114bc1a2736516c5ad60ef3aa9bd1b694886e3ca92d"
+checksum = "c57c477b645ee248b173bb1176b52dd528872f12c50375801a58aaf5ae91113f"
 dependencies = [
  "bstr",
  "itoa 1.0.11",
@@ -1352,9 +1353,9 @@ dependencies = [
 
 [[package]]
 name = "gix-diff"
-version = "0.48.0"
+version = "0.49.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a327be31a392144b60ab0b1c863362c32a1c8f7effdfa2141d5d5b6b916ef3bf"
+checksum = "a8e92566eccbca205a0a0f96ffb0327c061e85bc5c95abbcddfe177498aa04f6"
 dependencies = [
  "bstr",
  "gix-hash",
@@ -1364,9 +1365,9 @@ dependencies = [
 
 [[package]]
 name = "gix-dir"
-version = "0.10.0"
+version = "0.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "acd6a0618958f9cce78a32724f8e06c4f4a57ca7080f645736d53676dc9b4db9"
+checksum = "fba2ffbcf4bd34438e8a8367ccbc94870549903d1f193a14f47eb6b0967e1293"
 dependencies = [
  "bstr",
  "gix-discover",
@@ -1422,9 +1423,9 @@ dependencies = [
 
 [[package]]
 name = "gix-filter"
-version = "0.15.0"
+version = "0.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5108cc58d58b27df10ac4de7f31b2eb96d588a33e5eba23739b865f5d8db7995"
+checksum = "3d0ecdee5667f840ba20c7fe56d63f8e1dc1e6b3bfd296151fe5ef07c874790a"
 dependencies = [
  "bstr",
  "encoding_rs",
@@ -1443,9 +1444,9 @@ dependencies = [
 
 [[package]]
 name = "gix-fs"
-version = "0.12.0"
+version = "0.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "34740384d8d763975858fa2c176b68652a6fcc09f616e24e3ce967b0d370e4d8"
+checksum = "3b3d4fac505a621f97e5ce2c69fdc425742af00c0920363ca4074f0eb48b1db9"
 dependencies = [
  "fastrand",
  "gix-features",
@@ -1555,9 +1556,9 @@ dependencies = [
 
 [[package]]
 name = "gix-object"
-version = "0.46.0"
+version = "0.46.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "65d93e2bbfa83a307e47f45e45de7b6c04d7375a8bd5907b215f4bf45237d879"
+checksum = "e42d58010183ef033f31088479b4eb92b44fe341b35b62d39eb8b185573d77ea"
 dependencies = [
  "bstr",
  "gix-actor",
@@ -1565,6 +1566,7 @@ dependencies = [
  "gix-features",
  "gix-hash",
  "gix-hashtable",
+ "gix-path",
  "gix-utils",
  "gix-validate",
  "itoa 1.0.11",
@@ -1575,9 +1577,9 @@ dependencies = [
 
 [[package]]
 name = "gix-odb"
-version = "0.65.0"
+version = "0.66.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "93bed6e1b577c25a6bb8e6ecbf4df525f29a671ddf5f2221821a56a8dbeec4e3"
+checksum = "cb780eceb3372ee204469478de02eaa34f6ba98247df0186337e0333de97d0ae"
 dependencies = [
  "arc-swap",
  "gix-date",
@@ -1596,9 +1598,9 @@ dependencies = [
 
 [[package]]
 name = "gix-pack"
-version = "0.55.0"
+version = "0.56.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9b91fec04d359544fecbb8e85117ec746fbaa9046ebafcefb58cb74f20dc76d4"
+checksum = "4158928929be29cae7ab97afc8e820a932071a7f39d8ba388eed2380c12c566c"
 dependencies = [
  "clru",
  "gix-chunk",
@@ -1616,9 +1618,9 @@ dependencies = [
 
 [[package]]
 name = "gix-packetline"
-version = "0.18.1"
+version = "0.18.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8a720e5bebf494c3ceffa85aa89f57a5859450a0da0a29ebe89171e23543fa78"
+checksum = "911aeea8b2dabeed2f775af9906152a1f0109787074daf9e64224e3892dde453"
 dependencies = [
  "bstr",
  "faster-hex",
@@ -1668,9 +1670,9 @@ dependencies = [
 
 [[package]]
 name = "gix-prompt"
-version = "0.8.9"
+version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a7822afc4bc9c5fbbc6ce80b00f41c129306b7685cac3248dbfa14784960594"
+checksum = "82433a19aa44688e3bde05c692870eda50b5db053df53ed5ae6d8ea594a6babd"
 dependencies = [
  "gix-command",
  "gix-config-value",
@@ -1681,15 +1683,23 @@ dependencies = [
 
 [[package]]
 name = "gix-protocol"
-version = "0.46.1"
+version = "0.47.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a7e7e51a0dea531d3448c297e2fa919b2de187111a210c324b7e9f81508b8ca"
+checksum = "c84642e8b6fed7035ce9cc449593019c55b0ec1af7a5dce1ab8a0636eaaeb067"
 dependencies = [
  "bstr",
  "gix-credentials",
  "gix-date",
  "gix-features",
  "gix-hash",
+ "gix-lock",
+ "gix-negotiate",
+ "gix-object",
+ "gix-ref",
+ "gix-refspec",
+ "gix-revwalk",
+ "gix-shallow",
+ "gix-trace",
  "gix-transport",
  "gix-utils",
  "maybe-async",
@@ -1710,9 +1720,9 @@ dependencies = [
 
 [[package]]
 name = "gix-ref"
-version = "0.49.0"
+version = "0.49.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1eae462723686272a58f49501015ef7c0d67c3e042c20049d8dd9c7eff92efde"
+checksum = "a91b61776c839d0f1b7114901179afb0947aa7f4d30793ca1c56d335dfef485f"
 dependencies = [
  "gix-actor",
  "gix-features",
@@ -1745,9 +1755,9 @@ dependencies = [
 
 [[package]]
 name = "gix-revision"
-version = "0.31.0"
+version = "0.31.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "44488e0380847967bc3e3cacd8b22652e02ea1eb58afb60edd91847695cd2d8d"
+checksum = "61e1ddc474405a68d2ce8485705dd72fe6ce959f2f5fe718601ead5da2c8f9e7"
 dependencies = [
  "bitflags 2.6.0",
  "bstr",
@@ -1788,6 +1798,18 @@ dependencies = [
  "windows-sys 0.52.0",
 ]
 
+[[package]]
+name = "gix-shallow"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "88d2673242e87492cb6ff671f0c01f689061ca306c4020f137197f3abc84ce01"
+dependencies = [
+ "bstr",
+ "gix-hash",
+ "gix-lock",
+ "thiserror 2.0.3",
+]
+
 [[package]]
 name = "gix-submodule"
 version = "0.16.0"
@@ -1824,9 +1846,9 @@ checksum = "04bdde120c29f1fc23a24d3e115aeeea3d60d8e65bab92cc5f9d90d9302eb952"
 
 [[package]]
 name = "gix-transport"
-version = "0.43.1"
+version = "0.44.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "39a1a41357b7236c03e0c984147f823d87c3e445a8581bac7006df141577200b"
+checksum = "dd04d91e507a8713cfa2318d5a85d75b36e53a40379cc7eb7634ce400ecacbaf"
 dependencies = [
  "base64",
  "bstr",
@@ -1843,9 +1865,9 @@ dependencies = [
 
 [[package]]
 name = "gix-traverse"
-version = "0.43.0"
+version = "0.43.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3ff2ec9f779680f795363db1c563168b32b8d6728ec58564c628e85c92d29faf"
+checksum = "6ed47d648619e23e93f971d2bba0d10c1100e54ef95d2981d609907a8cabac89"
 dependencies = [
  "bitflags 2.6.0",
  "gix-commitgraph",
@@ -1860,13 +1882,14 @@ dependencies = [
 
 [[package]]
 name = "gix-url"
-version = "0.28.1"
+version = "0.28.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e09f97db3618fb8e473d7d97e77296b50aaee0ddcd6a867f07443e3e87391099"
+checksum = "d096fb733ba6bd3f5403dba8bd72bdd8809fe2b347b57844040b8f49c93492d9"
 dependencies = [
  "bstr",
  "gix-features",
  "gix-path",
+ "percent-encoding",
  "thiserror 2.0.3",
  "url",
 ]

Cargo.toml

@@ -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"

src/cargo/sources/git/oxide.rs

@@ -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/utils.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(_)
+        ))
     )
 }