Cargo-Patch is a Cargo Subcommand which allows patching dependencies using patch files.

Simply run:

cargo install cargo-patch

To patch a dependency one has to add the following to Cargo.toml:

[package.metadata.patch.serde]
version = "1.0"
patches = [
    "test.patch"
]

It specifies which dependency to patch (in this case serde) and one or more patchfiles to apply. Running:

cargo patch

will download the serde package specified in the dependency section to the target/patch folder and apply the given patches. To use the patched version one has to override the dependency using replace like this

[patch.crates-io]
serde = { path = './target/patch/serde-1.0.110' }

You can either use diff or git to create patch files. Important is that file paths are relative and inside the dependency.

[package.metadata.patch.serde]
version = "1.0"
patches = [
    { path = "generatedByGithub.patch", source = "GithubPrDiff" },
    { path = "generatedByGithub2.patch", source = "GithubPrDiff" },
    "test.patch",
    "test2.patch"
]

It's only possible to patch dependencies of binary crates as it is not possible for a subcommand to intercept the build process.