diff --git a/NEWS.md b/NEWS.md
index 6a3449f1..a57586d1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
 
 - Better estimation of time remaining, based on the time taken to test mutants so far, excluding the time for the baseline.
 
+- New: `--copy-vcs` option and config option will copy `.git` and other VCS directories, to accommodate trees whose tests depend on the contents or presence of the VCS directory.
+
 ## 24.11.2
 
 - Changed: `.gitignore` (and other git ignore files) are only consulted when copying the tree if it is contained within a directory with a `.git` directory.
diff --git a/book/src/SUMMARY.md b/book/src/SUMMARY.md
index e43e0e25..657cd221 100644
--- a/book/src/SUMMARY.md
+++ b/book/src/SUMMARY.md
@@ -17,7 +17,7 @@
   - [Listing and previewing mutations](list.md)
   - [Workspaces and packages](workspaces.md)
   - [Passing options to Cargo](cargo-args.md)
-  - [Build directories](build-dirs.md)
+  - [Copying the tree](build-dirs.md)
   - [Using nextest](nextest.md)
   - [Baseline tests](baseline.md)
   - [Testing in-place](in-place.md)
diff --git a/book/src/build-dirs.md b/book/src/build-dirs.md
index 09e562eb..4585da15 100644
--- a/book/src/build-dirs.md
+++ b/book/src/build-dirs.md
@@ -1,10 +1,18 @@
-# Build directories
+# Copying the tree
 
-cargo-mutants builds mutated code in a temporary directory, containing a copy of your source tree with each mutant successively applied. With `--jobs`, multiple build directories are used in parallel.
+By default, cargo-mutants copies your tree to a temporary directory before mutating and building it. This behavior is turned of by the [`--in-place`](in-place.md) option, which builds mutated code in the original source directory.
 
-## Build-in ignores
+When the [`--jobs`](parallelism.md) option is used, one build directory is created per job.
 
-Files or directories matching these patterns are not copied:
+Some filters are applied while copying the tree, which can be configured by options.
+
+## Troubleshooting tree copies
+
+If the baseline tests fail in the copied directory it is a good first debugging step to try building with `--in-place`.
+
+## `.git` and other version control directories
+
+By default, files or directories matching these patterns are not copied, because they can be large and typically are not needed to build the source:
 
     .git
     .hg
@@ -13,7 +21,9 @@ Files or directories matching these patterns are not copied:
     _darcs
     .pijul
 
-## gitignore
+If your tree's build or tests require the VCS directory then it can be copied with `--copy-vcs=true` or by setting `copy_vcs = true` in `.cargo/mutants.toml`.
+
+## `.gitignore`
 
 From 23.11.2, by default, cargo-mutants will not copy files that are excluded by gitignore patterns, to make copying faster in large trees.
 
@@ -22,3 +32,9 @@ gitignore filtering is only used within trees containing a `.git` directory.
 The filter, based on the [`ignore` crate](https://docs.rs/ignore/), also respects global git ignore configuration in the home directory, as well as `.gitignore` files within the tree.
 
 This behavior can be turned off with `--gitignore=false`, causing ignored files to be copied.
+
+Rust projects typically configure gitignore to exclude the `target/` directory.
+
+## `mutants.out`
+
+`mutants.out` and `mutants.out.old` are never copied, even if they're not covered by `.gitignore`.
diff --git a/src/build_dir.rs b/src/build_dir.rs
index 7cff8b71..2df19e95 100644
--- a/src/build_dir.rs
+++ b/src/build_dir.rs
@@ -57,7 +57,7 @@ impl BuildDir {
         let source_abs = source
             .canonicalize_utf8()
             .context("canonicalize source path")?;
-        let temp_dir = copy_tree(source, &name_base, options.gitignore, console)?;
+        let temp_dir = copy_tree(source, &name_base, options, console)?;
         let path: Utf8PathBuf = temp_dir
             .path()
             .to_owned()
diff --git a/src/config.rs b/src/config.rs
index 796d6094..e56b4919 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -29,6 +29,8 @@ use crate::Result;
 pub struct Config {
     /// Pass `--cap-lints` to rustc.
     pub cap_lints: bool,
+    /// Copy `.git` and other VCS directories to the build directory.
+    pub copy_vcs: Option<bool>,
     /// Generate these error values from functions returning Result.
     pub error_values: Vec<String>,
     /// Generate mutants from source files matching these globs.
diff --git a/src/copy_tree.rs b/src/copy_tree.rs
index 37661d7c..71a20808 100644
--- a/src/copy_tree.rs
+++ b/src/copy_tree.rs
@@ -9,6 +9,7 @@ use path_slash::PathExt;
 use tempfile::TempDir;
 use tracing::{debug, warn};
 
+use crate::options::Options;
 use crate::{check_interrupted, Console, Result};
 
 #[cfg(unix)]
@@ -21,28 +22,13 @@ mod windows;
 #[cfg(windows)]
 use windows::copy_symlink;
 
-/// Filenames excluded from being copied with the source.
-static SOURCE_EXCLUDE: &[&str] = &[
-    ".git",
-    ".hg",
-    ".bzr",
-    ".svn",
-    "_darcs",
-    ".pijul",
-    "mutants.out",
-    "mutants.out.old",
-];
+static VCS_DIRS: &[&str] = &[".git", ".hg", ".bzr", ".svn", "_darcs", ".pijul"];
 
 /// Copy a source tree, with some exclusions, to a new temporary directory.
-///
-/// If `git` is true, ignore files that are excluded by all the various `.gitignore`
-/// files.
-///
-/// Regardless, anything matching [`SOURCE_EXCLUDE`] is excluded.
 pub fn copy_tree(
     from_path: &Utf8Path,
     name_base: &str,
-    gitignore: bool,
+    options: &Options,
     console: &Console,
 ) -> Result<TempDir> {
     let mut total_bytes = 0;
@@ -58,13 +44,19 @@ pub fn copy_tree(
         .context("Convert path to UTF-8")?;
     console.start_copy(dest);
     let mut walk_builder = WalkBuilder::new(from_path);
+    let copy_vcs = options.copy_vcs; // for lifetime
     walk_builder
-        .standard_filters(gitignore)
+        .git_ignore(options.gitignore)
+        .git_exclude(options.gitignore)
+        .git_global(options.gitignore)
         .hidden(false) // copy hidden files
         .ignore(false) // don't use .ignore
         .require_git(true) // stop at git root; only read gitignore files inside git trees
-        .filter_entry(|entry| {
-            !SOURCE_EXCLUDE.contains(&entry.file_name().to_string_lossy().as_ref())
+        .filter_entry(move |entry| {
+            let name = entry.file_name().to_string_lossy();
+            name != "mutants.out"
+                && name != "mutants.out.old"
+                && (copy_vcs || !VCS_DIRS.contains(&name.as_ref()))
         });
     debug!(?walk_builder);
     for entry in walk_builder.build() {
@@ -115,12 +107,15 @@ pub fn copy_tree(
 
 #[cfg(test)]
 mod test {
+    // TODO: Maybe run these with $HOME set to a temp dir so that global git config has no effect?
+
     use std::fs::{create_dir, write};
 
     use camino::Utf8PathBuf;
     use tempfile::TempDir;
 
     use crate::console::Console;
+    use crate::options::Options;
     use crate::Result;
 
     use super::copy_tree;
@@ -139,7 +134,8 @@ mod test {
         create_dir(&src)?;
         write(src.join("main.rs"), "fn main() {}")?;
 
-        let dest_tmpdir = copy_tree(&a, "a", true, &Console::new())?;
+        let options = Options::from_arg_strs(["--gitignore=true"]);
+        let dest_tmpdir = copy_tree(&a, "a", &options, &Console::new())?;
         let dest = dest_tmpdir.path();
         assert!(dest.join("Cargo.toml").is_file());
         assert!(dest.join("src").is_dir());
@@ -147,4 +143,141 @@ mod test {
 
         Ok(())
     }
+
+    /// With `gitignore` set to `true`, but no `.git`, don't exclude anything.
+    #[test]
+    fn copy_with_gitignore_but_without_git_dir() -> Result<()> {
+        let tmp_dir = TempDir::new().unwrap();
+        let tmp = Utf8PathBuf::try_from(tmp_dir.path().to_owned()).unwrap();
+        write(tmp.join(".gitignore"), "foo\n")?;
+
+        write(tmp.join("Cargo.toml"), "[package]\nname = a")?;
+        let src = tmp.join("src");
+        create_dir(&src)?;
+        write(src.join("main.rs"), "fn main() {}")?;
+        write(tmp.join("foo"), "bar")?;
+
+        let options = Options::from_arg_strs(["--gitignore=true"]);
+        let dest_tmpdir = copy_tree(&tmp, "a", &options, &Console::new())?;
+        let dest = dest_tmpdir.path();
+        assert!(
+            dest.join("foo").is_file(),
+            "foo should be copied because gitignore is not used without .git"
+        );
+
+        Ok(())
+    }
+
+    /// With `gitignore` set to `true`, in a tree with `.git`, `.gitignore` is respected.
+    #[test]
+    fn copy_with_gitignore_and_git_dir() -> Result<()> {
+        let tmp_dir = TempDir::new().unwrap();
+        let tmp = Utf8PathBuf::try_from(tmp_dir.path().to_owned()).unwrap();
+        write(tmp.join(".gitignore"), "foo\n")?;
+        create_dir(tmp.join(".git"))?;
+
+        write(tmp.join("Cargo.toml"), "[package]\nname = a")?;
+        let src = tmp.join("src");
+        create_dir(&src)?;
+        write(src.join("main.rs"), "fn main() {}")?;
+        write(tmp.join("foo"), "bar")?;
+
+        let options = Options::from_arg_strs(["mutants", "--gitignore=true"]);
+        let dest_tmpdir = copy_tree(&tmp, "a", &options, &Console::new())?;
+        let dest = dest_tmpdir.path();
+        assert!(
+            !dest.join("foo").is_file(),
+            "foo should have been excluded by gitignore"
+        );
+
+        Ok(())
+    }
+
+    /// With `gitignore` set to `false`, patterns in that file have no effect.
+    #[test]
+    fn copy_without_gitignore() -> Result<()> {
+        let tmp_dir = TempDir::new().unwrap();
+        let tmp = Utf8PathBuf::try_from(tmp_dir.path().to_owned()).unwrap();
+        write(tmp.join(".gitignore"), "foo\n")?;
+        create_dir(tmp.join(".git"))?;
+
+        write(tmp.join("Cargo.toml"), "[package]\nname = a")?;
+        let src = tmp.join("src");
+        create_dir(&src)?;
+        write(src.join("main.rs"), "fn main() {}")?;
+        write(tmp.join("foo"), "bar")?;
+
+        let options = Options::from_arg_strs(["mutants", "--gitignore=false"]);
+        let dest_tmpdir = copy_tree(&tmp, "a", &options, &Console::new())?;
+        let dest = dest_tmpdir.path();
+        // gitignore didn't exclude `foo`
+        assert!(dest.join("foo").is_file());
+
+        Ok(())
+    }
+
+    #[test]
+    fn dont_copy_git_dir_or_mutants_out_by_default() -> Result<()> {
+        let tmp_dir = TempDir::new().unwrap();
+        let tmp = Utf8PathBuf::try_from(tmp_dir.path().to_owned()).unwrap();
+        create_dir(tmp.join(".git"))?;
+        write(tmp.join(".git/foo"), "bar")?;
+        create_dir(tmp.join("mutants.out"))?;
+        write(tmp.join("mutants.out/foo"), "bar")?;
+
+        write(tmp.join("Cargo.toml"), "[package]\nname = a")?;
+        let src = tmp.join("src");
+        create_dir(&src)?;
+        write(src.join("main.rs"), "fn main() {}")?;
+
+        let options = Options::from_arg_strs(["mutants"]);
+        let dest_tmpdir = copy_tree(&tmp, "a", &options, &Console::new())?;
+        let dest = dest_tmpdir.path();
+        assert!(!dest.join(".git").is_dir(), ".git should not be copied");
+        assert!(
+            !dest.join(".git/foo").is_file(),
+            ".git/foo should not be copied"
+        );
+        assert!(
+            !dest.join("mutants.out").exists(),
+            "mutants.out should not be copied"
+        );
+        assert!(
+            dest.join("Cargo.toml").is_file(),
+            "Cargo.toml should be copied"
+        );
+
+        Ok(())
+    }
+
+    #[test]
+    fn copy_git_dir_when_requested() -> Result<()> {
+        let tmp_dir = TempDir::new().unwrap();
+        let tmp = Utf8PathBuf::try_from(tmp_dir.path().to_owned()).unwrap();
+        create_dir(tmp.join(".git"))?;
+        write(tmp.join(".git/foo"), "bar")?;
+        create_dir(tmp.join("mutants.out"))?;
+        write(tmp.join("mutants.out/foo"), "bar")?;
+
+        write(tmp.join("Cargo.toml"), "[package]\nname = a")?;
+        let src = tmp.join("src");
+        create_dir(&src)?;
+        write(src.join("main.rs"), "fn main() {}")?;
+
+        let options = Options::from_arg_strs(["mutants", "--copy-vcs=true"]);
+        let dest_tmpdir = copy_tree(&tmp, "a", &options, &Console::new())?;
+        let dest = dest_tmpdir.path();
+        assert!(dest.join(".git").is_dir(), ".git should be copied");
+        assert!(dest.join(".git/foo").is_file(), ".git/foo should be copied");
+        assert!(
+            !dest.join("mutants.out").exists(),
+            "mutants.out should not be copied"
+        );
+        assert!(
+            dest.join("Cargo.toml").is_file(),
+            "Cargo.toml should be copied"
+        );
+
+        Ok(())
+    }
 }
diff --git a/src/main.rs b/src/main.rs
index 74629093..b6c495ad 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -144,6 +144,15 @@ pub struct Args {
     )]
     colors: Colors,
 
+    /// Copy `.git` and other VCS directories to the build directory.
+    ///
+    /// This is useful if you have tests that depend on the presence of these directories.
+    ///
+    /// Known VCS directories are
+    /// `.git`, `.hg`, `.bzr`, `.svn`, `_darcs`, `.pijul`.
+    #[arg(long, help_heading = "Copying", visible_alias = "copy_git")]
+    copy_vcs: Option<bool>,
+
     /// Show the mutation diffs.
     #[arg(long, help_heading = "Filters")]
     diff: bool,
diff --git a/src/options.rs b/src/options.rs
index dfccdc7d..8ee391b4 100644
--- a/src/options.rs
+++ b/src/options.rs
@@ -41,6 +41,9 @@ pub struct Options {
     /// Don't run the tests, just see if each mutant builds.
     pub check_only: bool,
 
+    /// Copy `.git` and other VCS directories to build directories.
+    pub copy_vcs: bool,
+
     /// Don't copy files matching gitignore patterns to build directories.
     pub gitignore: bool,
 
@@ -285,6 +288,7 @@ impl Options {
             cap_lints: args.cap_lints.unwrap_or(config.cap_lints),
             check_only: args.check,
             colors: args.colors,
+            copy_vcs: args.copy_vcs.or(config.copy_vcs).unwrap_or(false),
             emit_json: args.json,
             emit_diffs: args.diff,
             error_values: join_slices(&args.error, &config.error_values),
@@ -837,4 +841,27 @@ mod test {
         // In this case the default is not used
         assert_eq!(options.skip_calls, ["x", "y", "with_capacity"]);
     }
+
+    #[test]
+    fn copy_vcs() {
+        let args = Args::parse_from(["mutants", "--copy-vcs=true"]);
+        let config = Config::default();
+        let options = Options::new(&args, &config).unwrap();
+        assert!(options.copy_vcs);
+
+        let args = Args::parse_from(["mutants", "--copy-vcs=false"]);
+        let config = Config::default();
+        let options = Options::new(&args, &config).unwrap();
+        assert!(!options.copy_vcs);
+
+        let args = Args::parse_from(["mutants"]);
+        let config = Config::from_str("copy_vcs = true").unwrap();
+        let options = Options::new(&args, &config).unwrap();
+        assert!(options.copy_vcs);
+
+        let args = Args::parse_from(["mutants"]);
+        let config = Config::from_str("").unwrap();
+        let options = Options::new(&args, &config).unwrap();
+        assert!(!options.copy_vcs);
+    }
 }