diff --git a/.bazelci/presubmit.yml b/.bazelci/presubmit.yml
index a08e71c25e..f4f0902e51 100644
--- a/.bazelci/presubmit.yml
+++ b/.bazelci/presubmit.yml
@@ -36,6 +36,21 @@ default_windows_targets: &default_windows_targets
   - "//..."
   - "-//test/proto/..."
   - "-//test/unit/pipelined_compilation/..."
+default_windows_no_runfiles_targets: &default_windows_no_runfiles_targets
+  - "--" # Allows negative patterns; hack for https://github.com/bazelbuild/continuous-integration/pull/245
+  - "//..."
+  # TODO: https://github.com/bazelbuild/rules_rust/issues/1156
+  - "-//crate_universe/..."
+  - "-//test/chained_direct_deps:mod3_doc_test"
+  - "-//test/out_dir_in_tests:demo_lib_doc_test"
+  - "-//test/proto/..."
+  - "-//test/rustc_env_files:output_test"
+  - "-//test/test_env_launcher:test"
+  - "-//test/test_env:test_manifest_dir"
+  - "-//test/test_env:test_run"
+  - "-//test/unit/pipelined_compilation/..."
+  - "-//test/unit/rustdoc/..."
+  - "-//tools/runfiles/..."
 crate_universe_vendor_example_targets: &crate_universe_vendor_example_targets
   - "//vendor_external:crates_vendor"
   - "//vendor_local_manifests:crates_vendor"
@@ -58,6 +73,7 @@ split_coverage_postprocessing_shell_commands: &split_coverage_postprocessing_she
   - echo "build --//rust/settings:experimental_use_coverage_metadata_files" >> user.bazelrc
 tasks:
   ubuntu2004:
+    platform: ubuntu2004
     build_targets: *default_linux_targets
     test_targets: *default_linux_targets
     coverage_targets: *default_linux_targets
@@ -65,19 +81,31 @@ tasks:
     run_targets:
       - //test:query_test_binary
   rbe_ubuntu2004:
+    platform: rbe_ubuntu2004
     shell_commands:
       - sed -i 's/^# load("@bazel_ci_rules/load("@bazel_ci_rules/' WORKSPACE.bazel
       - sed -i 's/^# rbe_preconfig/rbe_preconfig/' WORKSPACE.bazel
     build_targets: *default_linux_targets
     test_targets: *default_linux_targets
   macos:
+    platform: macos
     build_targets: *default_macos_targets
     test_targets: *default_macos_targets
     coverage_targets: *default_macos_targets
     post_shell_commands: *coverage_validation_post_shell_commands
   windows:
+    platform: windows
     build_targets: *default_windows_targets
     test_targets: *default_windows_targets
+  windows_no_runfiles:
+    name: No Runfiles
+    platform: windows
+    build_flags:
+      - "--noenable_runfiles"
+    test_flags:
+      - "--noenable_runfiles"
+    build_targets: *default_windows_no_runfiles_targets
+    test_targets: *default_windows_no_runfiles_targets
   ubuntu2004_split_coverage_postprocessing:
     name: Split Coverage Postprocessing
     platform: ubuntu2004
@@ -171,6 +199,19 @@ tasks:
       - "--config=clippy"
     build_targets: *default_windows_targets
     test_targets: *default_windows_targets
+  windows_no_runfiles_with_aspects:
+    name: No Runfiles With Aspects
+    platform: windows
+    build_flags:
+      - "--noenable_runfiles"
+      - "--config=rustfmt"
+      - "--config=clippy"
+    test_flags:
+      - "--noenable_runfiles"
+      - "--config=rustfmt"
+      - "--config=clippy"
+    build_targets: *default_windows_no_runfiles_targets
+    test_targets: *default_windows_no_runfiles_targets
   windows_rolling_with_aspects:
     name: "Windows Rolling Bazel Version With Aspects"
     platform: windows
@@ -610,7 +651,7 @@ tasks:
     environment:
       # This ndk version matches with rules_android_ndk repo's CI
       # https://github.com/bazelbuild/rules_android_ndk/blob/877c68ef34c9f3353028bf490d269230c1990483/.bazelci/presubmit.yml#L37
-      # The ndk is installed by this script 
+      # The ndk is installed by this script
       # https://github.com/bazelbuild/continuous-integration/blob/ba56013373821feadd9f2eaa6b81eb19528795f0/macos/mac-android.sh
       ANDROID_NDK_HOME: /opt/android-ndk-r25b
   android_examples_macos:
@@ -625,7 +666,7 @@ tasks:
     environment:
       # This ndk version matches with rules_android_ndk repo's CI
       # https://github.com/bazelbuild/rules_android_ndk/blob/877c68ef34c9f3353028bf490d269230c1990483/.bazelci/presubmit.yml#L42
-      # The ndk is installed by this script 
+      # The ndk is installed by this script
       # https://github.com/bazelbuild/continuous-integration/blob/ba56013373821feadd9f2eaa6b81eb19528795f0/macos/mac-android.sh
       ANDROID_NDK_HOME: /Users/buildkite/android-ndk-r25b
   ios_examples:
diff --git a/cargo/cargo_build_script_runner/lib.rs b/cargo/cargo_build_script_runner/lib.rs
index 3739a1778d..201e90144e 100644
--- a/cargo/cargo_build_script_runner/lib.rs
+++ b/cargo/cargo_build_script_runner/lib.rs
@@ -124,7 +124,9 @@ impl BuildScriptOutput {
     pub fn outputs_from_command(
         cmd: &mut Command,
     ) -> Result<(Vec<BuildScriptOutput>, Output), Output> {
-        let child_output = cmd.output().expect("Unable to start binary");
+        let child_output = cmd
+            .output()
+            .unwrap_or_else(|e| panic!("Unable to start command:\n{:?}\n{:#?}", e, cmd));
         if child_output.status.success() {
             let reader = BufReader::new(child_output.stdout.as_slice());
             let output = Self::outputs_from_reader(reader);
diff --git a/cargo/private/BUILD.bazel b/cargo/private/BUILD.bazel
index 6a1aab653c..2b7e6de7dd 100644
--- a/cargo/private/BUILD.bazel
+++ b/cargo/private/BUILD.bazel
@@ -1,7 +1,13 @@
 load("@bazel_skylib//:bzl_library.bzl", "bzl_library")
+load(":runfiles_enabled.bzl", "runfiles_enabled_build_setting")
 
 bzl_library(
     name = "bzl_lib",
     srcs = glob(["**/*.bzl"]),
     visibility = ["//:__subpackages__"],
 )
+
+runfiles_enabled_build_setting(
+    name = "runfiles_enabled",
+    visibility = ["//visibility:public"],
+)
diff --git a/cargo/private/cargo_build_script.bzl b/cargo/private/cargo_build_script.bzl
index 56f64994af..8d08395c85 100644
--- a/cargo/private/cargo_build_script.bzl
+++ b/cargo/private/cargo_build_script.bzl
@@ -23,6 +23,7 @@ load(
     "find_toolchain",
     _name_to_crate_name = "name_to_crate_name",
 )
+load(":runfiles_enabled.bzl", "is_runfiles_enabled", "runfiles_enabled_attr")
 
 # Reexport for cargo_build_script_wrapper.bzl
 name_to_crate_name = _name_to_crate_name
@@ -198,6 +199,39 @@ def _feature_enabled(ctx, feature_name, default = False):
 
     return default
 
+def _rlocationpath(file, workspace_name):
+    if file.short_path.startswith("../"):
+        return file.short_path[len("../"):]
+
+    return "{}/{}".format(workspace_name, file.short_path)
+
+def _create_runfiles_dir(ctx, script):
+    runfiles_dir = ctx.actions.declare_directory("{}.cargo_runfiles".format(ctx.label.name))
+
+    workspace_name = ctx.label.workspace_name
+    if not workspace_name:
+        workspace_name = ctx.workspace_name
+
+    def _runfiles_map(file):
+        return "{}={}".format(file.path, _rlocationpath(file, workspace_name))
+
+    runfiles = script[DefaultInfo].default_runfiles
+
+    args = ctx.actions.args()
+    args.use_param_file("@%s", use_always = True)
+    args.add(runfiles_dir.path)
+    args.add_all(runfiles.files, map_each = _runfiles_map, allow_closure = True)
+
+    ctx.actions.run(
+        mnemonic = "CargoBuildScriptRunfilesDir",
+        executable = ctx.executable._runfiles_maker,
+        arguments = [args],
+        inputs = runfiles.files,
+        outputs = [runfiles_dir],
+    )
+
+    return runfiles_dir
+
 def _cargo_build_script_impl(ctx):
     """The implementation for the `cargo_build_script` rule.
 
@@ -208,6 +242,7 @@ def _cargo_build_script_impl(ctx):
         list: A list containing a BuildInfo provider
     """
     script = ctx.executable.script
+    script_info = ctx.attr.script[CargoBuildScriptRunfilesInfo]
     toolchain = find_toolchain(ctx)
     out_dir = ctx.actions.declare_directory(ctx.label.name + ".out_dir")
     env_out = ctx.actions.declare_file(ctx.label.name + ".env")
@@ -215,9 +250,27 @@ def _cargo_build_script_impl(ctx):
     flags_out = ctx.actions.declare_file(ctx.label.name + ".flags")
     link_flags = ctx.actions.declare_file(ctx.label.name + ".linkflags")
     link_search_paths = ctx.actions.declare_file(ctx.label.name + ".linksearchpaths")  # rustc-link-search, propagated from transitive dependencies
-    manifest_dir = "%s.runfiles/%s/%s" % (script.path, ctx.label.workspace_name or ctx.workspace_name, ctx.label.package)
     compilation_mode_opt_level = get_compilation_mode_opts(ctx, toolchain).opt_level
 
+    script_tools = []
+    script_data = []
+    for target in script_info.data:
+        script_data.append(target[DefaultInfo].files)
+        script_data.append(target[DefaultInfo].default_runfiles.files)
+    for target in script_info.tools:
+        script_tools.append(target[DefaultInfo].files)
+        script_tools.append(target[DefaultInfo].default_runfiles.files)
+
+    workspace_name = ctx.label.workspace_name
+    if not workspace_name:
+        workspace_name = ctx.workspace_name
+
+    manifest_dir = "{}.runfiles/{}/{}".format(script.path, workspace_name, ctx.label.package)
+    if not is_runfiles_enabled(ctx.attr):
+        runfiles_dir = _create_runfiles_dir(ctx, ctx.attr.script)
+        script_data.append(depset([runfiles_dir]))
+        manifest_dir = "{}/{}/{}".format(runfiles_dir.path, workspace_name, ctx.label.package)
+
     streams = struct(
         stdout = ctx.actions.declare_file(ctx.label.name + ".stdout.log"),
         stderr = ctx.actions.declare_file(ctx.label.name + ".stderr.log"),
@@ -331,8 +384,6 @@ def _cargo_build_script_impl(ctx):
             variables = getattr(target[platform_common.TemplateVariableInfo], "variables", depset([]))
             env.update(variables)
 
-    script_info = ctx.attr.script[CargoBuildScriptRunfilesInfo]
-
     _merge_env_dict(env, expand_dict_value_locations(
         ctx,
         ctx.attr.build_script_env,
@@ -343,15 +394,6 @@ def _cargo_build_script_impl(ctx):
         script_info.tools,
     ))
 
-    script_tools = []
-    script_data = []
-    for target in script_info.data:
-        script_data.append(target[DefaultInfo].files)
-        script_data.append(target[DefaultInfo].default_runfiles.files)
-    for target in script_info.tools:
-        script_tools.append(target[DefaultInfo].files)
-        script_tools.append(target[DefaultInfo].default_runfiles.files)
-
     tools = depset(
         direct = [
             script,
@@ -379,6 +421,7 @@ def _cargo_build_script_impl(ctx):
     args.add(ctx.attr.rundir)
 
     build_script_inputs = []
+
     for dep in ctx.attr.link_deps:
         if rust_common.dep_info in dep and dep[rust_common.dep_info].dep_env:
             dep_env_file = dep[rust_common.dep_info].dep_env
@@ -520,7 +563,12 @@ cargo_build_script = rule(
         "_experimental_symlink_execroot": attr.label(
             default = Label("//cargo/settings:experimental_symlink_execroot"),
         ),
-    },
+        "_runfiles_maker": attr.label(
+            cfg = "exec",
+            executable = True,
+            default = Label("//cargo/private/runfiles_maker"),
+        ),
+    } | runfiles_enabled_attr(),
     fragments = ["cpp"],
     toolchains = [
         str(Label("//rust:toolchain_type")),
diff --git a/cargo/private/runfiles_enabled.bzl b/cargo/private/runfiles_enabled.bzl
new file mode 100644
index 0000000000..27138cf2eb
--- /dev/null
+++ b/cargo/private/runfiles_enabled.bzl
@@ -0,0 +1,167 @@
+"""A small utility module dedicated to detecting whether or not the `--enable_runfiles` and `--windows_enable_symlinks` flag are enabled
+"""
+
+load("@bazel_skylib//lib:selects.bzl", "selects")
+load("@bazel_skylib//rules:common_settings.bzl", "bool_setting")
+
+RunfilesEnabledInfo = provider(
+    doc = "A singleton provider that contains the raw value of a build setting",
+    fields = {
+        "value": "The value of the build setting in the current configuration. " +
+                 "This value may come from the command line or an upstream transition, " +
+                 "or else it will be the build setting's default.",
+    },
+)
+
+def _runfiles_enabled_setting_impl(ctx):
+    return RunfilesEnabledInfo(value = ctx.attr.value)
+
+runfiles_enabled_setting = rule(
+    implementation = _runfiles_enabled_setting_impl,
+    doc = "A bool-typed build setting that cannot be set on the command line",
+    attrs = {
+        "value": attr.bool(
+            doc = "A boolean value",
+            mandatory = True,
+        ),
+    },
+)
+
+_RUNFILES_ENABLED_ATTR_NAME = "_runfiles_enabled"
+
+def runfiles_enabled_attr(default = Label("//cargo/private:runfiles_enabled")):
+    return {
+        _RUNFILES_ENABLED_ATTR_NAME: attr.label(
+            doc = "A flag representing whether or not runfiles are enabled.",
+            providers = [RunfilesEnabledInfo],
+            default = default,
+            cfg = "exec",
+        ),
+    }
+
+def runfiles_enabled_build_setting(name, **kwargs):
+    """Define a build setting identifying if runfiles are enabled.
+
+    Args:
+        name (str): The name of the build setting
+        **kwargs: Additional keyword arguments for the target.
+    """
+    native.config_setting(
+        name = "{}__enable_runfiles".format(name),
+        values = {"enable_runfiles": "true"},
+    )
+
+    native.config_setting(
+        name = "{}__disable_runfiles".format(name),
+        values = {"enable_runfiles": "false"},
+    )
+
+    bool_setting(
+        name = "{}__always_true".format(name),
+        build_setting_default = True,
+    )
+
+    native.config_setting(
+        name = "{}__always_true_setting".format(name),
+        flag_values = {":{}__always_true".format(name): "True"},
+    )
+
+    native.config_setting(
+        name = "{}__always_false_setting".format(name),
+        flag_values = {":{}__always_true".format(name): "False"},
+    )
+
+    # There is no way to query a setting that is unset. By utilizing constant
+    # settings, we can filter to a fallback setting where no known value is
+    # defined.
+    native.alias(
+        name = "{}__unset_runfiles".format(name),
+        actual = select({
+            ":{}__disable_runfiles".format(name): ":{}__always_false_setting".format(name),
+            ":{}__enable_runfiles".format(name): ":{}__always_false_setting".format(name),
+            "//conditions:default": ":{}__always_true_setting".format(name),
+        }),
+    )
+
+    selects.config_setting_group(
+        name = "{}__windows_enable_runfiles".format(name),
+        match_all = [
+            ":{}__enable_runfiles".format(name),
+            "@platforms//os:windows",
+        ],
+    )
+
+    selects.config_setting_group(
+        name = "{}__windows_disable_runfiles".format(name),
+        match_all = [
+            ":{}__disable_runfiles".format(name),
+            "@platforms//os:windows",
+        ],
+    )
+
+    selects.config_setting_group(
+        name = "{}__windows_unset_runfiles".format(name),
+        match_all = [
+            ":{}__unset_runfiles".format(name),
+            "@platforms//os:windows",
+        ],
+    )
+
+    native.alias(
+        name = "{}__unix".format(name),
+        actual = select({
+            "@platforms//os:windows": ":{}__always_false_setting".format(name),
+            "//conditions:default": ":{}__always_true_setting".format(name),
+        }),
+    )
+
+    selects.config_setting_group(
+        name = "{}__unix_enable_runfiles".format(name),
+        match_all = [
+            ":{}__enable_runfiles".format(name),
+            ":{}__unix".format(name),
+        ],
+    )
+
+    selects.config_setting_group(
+        name = "{}__unix_disable_runfiles".format(name),
+        match_all = [
+            ":{}__disable_runfiles".format(name),
+            ":{}__unix".format(name),
+        ],
+    )
+
+    selects.config_setting_group(
+        name = "{}__unix_unset_runfiles".format(name),
+        match_all = [
+            ":{}__unset_runfiles".format(name),
+            ":{}__unix".format(name),
+        ],
+    )
+
+    runfiles_enabled_setting(
+        name = name,
+        value = select({
+            ":{}__windows_enable_runfiles".format(name): True,
+            ":{}__windows_disable_runfiles".format(name): False,
+            ":{}__windows_unset_runfiles".format(name): False,
+            ":{}__unix_enable_runfiles".format(name): True,
+            ":{}__unix_disable_runfiles".format(name): False,
+            ":{}__unix_unset_runfiles".format(name): True,
+            "//conditions:default": True,
+        }),
+        **kwargs
+    )
+
+def is_runfiles_enabled(attr):
+    """Determine whether or not runfiles are enabled.
+
+    Args:
+        attr (struct): A rule's struct of attributes (`ctx.attr`)
+    Returns:
+        bool: The enable_runfiles value.
+    """
+
+    runfiles_enabled = getattr(attr, _RUNFILES_ENABLED_ATTR_NAME, None)
+
+    return runfiles_enabled[RunfilesEnabledInfo].value if runfiles_enabled else True
diff --git a/cargo/private/runfiles_maker/BUILD.bazel b/cargo/private/runfiles_maker/BUILD.bazel
new file mode 100644
index 0000000000..3b3df766c2
--- /dev/null
+++ b/cargo/private/runfiles_maker/BUILD.bazel
@@ -0,0 +1,8 @@
+load("//rust:defs.bzl", "rust_binary")
+
+rust_binary(
+    name = "runfiles_maker",
+    srcs = ["runfiles_maker.rs"],
+    edition = "2021",
+    visibility = ["//visibility:public"],
+)
diff --git a/cargo/private/runfiles_maker/runfiles_maker.rs b/cargo/private/runfiles_maker/runfiles_maker.rs
new file mode 100644
index 0000000000..9dea797c69
--- /dev/null
+++ b/cargo/private/runfiles_maker/runfiles_maker.rs
@@ -0,0 +1,71 @@
+//! A tool for building runfiles directories for Bazel environments that don't
+//! support runfiles or have runfiles enabled.
+
+use std::collections::BTreeMap;
+use std::path::PathBuf;
+
+struct Args {
+    pub output_dir: PathBuf,
+    pub runfiles: BTreeMap<PathBuf, PathBuf>,
+}
+
+impl Args {
+    fn parse() -> Self {
+        let args_file = std::env::args().nth(1).expect("No args file was passed.");
+
+        let content = std::fs::read_to_string(
+            args_file
+                .strip_prefix('@')
+                .expect("Param files should start with @"),
+        )
+        .unwrap();
+        let mut args = content.lines();
+
+        let output_dir = PathBuf::from(
+            args.next()
+                .unwrap_or_else(|| panic!("Not enough arguments provided.")),
+        );
+        let runfiles = args
+            .map(|s| {
+                let s = if s.starts_with('\'') && s.ends_with('\'') {
+                    s.trim_matches('\'')
+                } else {
+                    s
+                };
+                let (src, dest) = s
+                    .split_once('=')
+                    .unwrap_or_else(|| panic!("Unexpected runfiles argument: {}", s));
+                (PathBuf::from(src), PathBuf::from(dest))
+            })
+            .collect::<BTreeMap<_, _>>();
+
+        assert!(!runfiles.is_empty(), "No runfiles found");
+
+        Args {
+            output_dir,
+            runfiles,
+        }
+    }
+}
+
+fn main() {
+    let args = Args::parse();
+
+    for (src, dest) in args.runfiles.iter() {
+        let out_dest = args.output_dir.join(dest);
+        std::fs::create_dir_all(
+            out_dest
+                .parent()
+                .expect("The output location should have a valid parent."),
+        )
+        .expect("Failed to create output directory");
+        std::fs::copy(src, &out_dest).unwrap_or_else(|e| {
+            panic!(
+                "Failed to copy file {} -> {}\n{:?}",
+                src.display(),
+                out_dest.display(),
+                e
+            )
+        });
+    }
+}
diff --git a/docs/src/index.md b/docs/src/index.md
index 1045dca333..53ee5cbd71 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -20,7 +20,7 @@ Note that rules_rust bzlmod support is still a work in progress. Most features s
 To use `rules_rust` in a project using bzlmod, add the following to your `MODULE.bazel` file:
 
 ```python
-bazel_dep(name = "rules_rust", version = "0.48.0")
+bazel_dep(name = "rules_rust", version = "0.50.1")
 ```
 
 Don't forget to substitute in your desired release's version number.
@@ -36,8 +36,8 @@ load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
 # https://github.com/bazelbuild/rules_rust/releases
 http_archive(
     name = "rules_rust",
-    integrity = "sha256-Weev1uz2QztBlDA88JX6A1N72SucD1V8lBsaliM0TTg=",
-    urls = ["https://github.com/bazelbuild/rules_rust/releases/download/0.48.0/rules_rust-v0.48.0.tar.gz"],
+    integrity = "sha256-Log/YgrGjboS4tCqQPBA58VPyFcnCn/IZm+xxKTZrn0=",
+    urls = ["https://github.com/bazelbuild/rules_rust/releases/download/0.50.1/rules_rust-v0.50.1.tar.gz"],
 )
 
 load("@rules_rust//rust:repositories.bzl", "rules_rust_dependencies", "rust_register_toolchains")
@@ -57,7 +57,7 @@ To build with a particular version of the Rust compiler, pass that version to [`
 rust_register_toolchains(
     edition = "2021",
     versions = [
-        "1.79.0"
+        "1.79.0",
     ],
 )
 ```
diff --git a/examples/crate_universe/cargo_aliases/.bazelrc b/examples/crate_universe/cargo_aliases/.bazelrc
deleted file mode 100644
index a67f1baf7f..0000000000
--- a/examples/crate_universe/cargo_aliases/.bazelrc
+++ /dev/null
@@ -1,25 +0,0 @@
-# A config file containing Bazel settings
-
-# Required on windows
-common --enable_platform_specific_config
-startup --windows_enable_symlinks
-build:windows --enable_runfiles
-
-# Enable rustfmt
-build:strict --aspects=@rules_rust//rust:defs.bzl%rustfmt_aspect
-build:strict --output_groups=+rustfmt_checks
-
-# Enable clippy
-build:strict --aspects=@rules_rust//rust:defs.bzl%rust_clippy_aspect
-build:strict --output_groups=+clippy_checks
-
-# TODO: migrate all dependencies from WORKSPACE to MODULE.bazel
-# https://github.com/bazelbuild/rules_rust/issues/2181
-common --noenable_bzlmod
-
-# This isn't currently the defaut in Bazel, but we enable it to test we'll be ready if/when it flips.
-build --incompatible_disallow_empty_glob
-
-# This import should always be last to allow users to override
-# settings for local development.
-try-import %workspace%/user.bazelrc
diff --git a/examples/crate_universe/cargo_remote/.bazelrc b/examples/crate_universe/cargo_remote/.bazelrc
deleted file mode 100644
index a67f1baf7f..0000000000
--- a/examples/crate_universe/cargo_remote/.bazelrc
+++ /dev/null
@@ -1,25 +0,0 @@
-# A config file containing Bazel settings
-
-# Required on windows
-common --enable_platform_specific_config
-startup --windows_enable_symlinks
-build:windows --enable_runfiles
-
-# Enable rustfmt
-build:strict --aspects=@rules_rust//rust:defs.bzl%rustfmt_aspect
-build:strict --output_groups=+rustfmt_checks
-
-# Enable clippy
-build:strict --aspects=@rules_rust//rust:defs.bzl%rust_clippy_aspect
-build:strict --output_groups=+clippy_checks
-
-# TODO: migrate all dependencies from WORKSPACE to MODULE.bazel
-# https://github.com/bazelbuild/rules_rust/issues/2181
-common --noenable_bzlmod
-
-# This isn't currently the defaut in Bazel, but we enable it to test we'll be ready if/when it flips.
-build --incompatible_disallow_empty_glob
-
-# This import should always be last to allow users to override
-# settings for local development.
-try-import %workspace%/user.bazelrc
diff --git a/examples/crate_universe/cargo_workspace/.bazelrc b/examples/crate_universe/cargo_workspace/.bazelrc
deleted file mode 100644
index a67f1baf7f..0000000000
--- a/examples/crate_universe/cargo_workspace/.bazelrc
+++ /dev/null
@@ -1,25 +0,0 @@
-# A config file containing Bazel settings
-
-# Required on windows
-common --enable_platform_specific_config
-startup --windows_enable_symlinks
-build:windows --enable_runfiles
-
-# Enable rustfmt
-build:strict --aspects=@rules_rust//rust:defs.bzl%rustfmt_aspect
-build:strict --output_groups=+rustfmt_checks
-
-# Enable clippy
-build:strict --aspects=@rules_rust//rust:defs.bzl%rust_clippy_aspect
-build:strict --output_groups=+clippy_checks
-
-# TODO: migrate all dependencies from WORKSPACE to MODULE.bazel
-# https://github.com/bazelbuild/rules_rust/issues/2181
-common --noenable_bzlmod
-
-# This isn't currently the defaut in Bazel, but we enable it to test we'll be ready if/when it flips.
-build --incompatible_disallow_empty_glob
-
-# This import should always be last to allow users to override
-# settings for local development.
-try-import %workspace%/user.bazelrc
diff --git a/examples/crate_universe/multi_package/.bazelrc b/examples/crate_universe/multi_package/.bazelrc
deleted file mode 100644
index a67f1baf7f..0000000000
--- a/examples/crate_universe/multi_package/.bazelrc
+++ /dev/null
@@ -1,25 +0,0 @@
-# A config file containing Bazel settings
-
-# Required on windows
-common --enable_platform_specific_config
-startup --windows_enable_symlinks
-build:windows --enable_runfiles
-
-# Enable rustfmt
-build:strict --aspects=@rules_rust//rust:defs.bzl%rustfmt_aspect
-build:strict --output_groups=+rustfmt_checks
-
-# Enable clippy
-build:strict --aspects=@rules_rust//rust:defs.bzl%rust_clippy_aspect
-build:strict --output_groups=+clippy_checks
-
-# TODO: migrate all dependencies from WORKSPACE to MODULE.bazel
-# https://github.com/bazelbuild/rules_rust/issues/2181
-common --noenable_bzlmod
-
-# This isn't currently the defaut in Bazel, but we enable it to test we'll be ready if/when it flips.
-build --incompatible_disallow_empty_glob
-
-# This import should always be last to allow users to override
-# settings for local development.
-try-import %workspace%/user.bazelrc
diff --git a/examples/crate_universe/no_cargo_manifests/.bazelrc b/examples/crate_universe/no_cargo_manifests/.bazelrc
deleted file mode 100644
index a67f1baf7f..0000000000
--- a/examples/crate_universe/no_cargo_manifests/.bazelrc
+++ /dev/null
@@ -1,25 +0,0 @@
-# A config file containing Bazel settings
-
-# Required on windows
-common --enable_platform_specific_config
-startup --windows_enable_symlinks
-build:windows --enable_runfiles
-
-# Enable rustfmt
-build:strict --aspects=@rules_rust//rust:defs.bzl%rustfmt_aspect
-build:strict --output_groups=+rustfmt_checks
-
-# Enable clippy
-build:strict --aspects=@rules_rust//rust:defs.bzl%rust_clippy_aspect
-build:strict --output_groups=+clippy_checks
-
-# TODO: migrate all dependencies from WORKSPACE to MODULE.bazel
-# https://github.com/bazelbuild/rules_rust/issues/2181
-common --noenable_bzlmod
-
-# This isn't currently the defaut in Bazel, but we enable it to test we'll be ready if/when it flips.
-build --incompatible_disallow_empty_glob
-
-# This import should always be last to allow users to override
-# settings for local development.
-try-import %workspace%/user.bazelrc
diff --git a/rust/private/rustc.bzl b/rust/private/rustc.bzl
index 5836040334..c82c236bb2 100644
--- a/rust/private/rustc.bzl
+++ b/rust/private/rustc.bzl
@@ -329,6 +329,7 @@ def collect_deps(
                 transitive_build_infos.append(depset([build_info]))
                 if build_info.link_search_paths:
                     transitive_link_search_paths.append(depset([build_info.link_search_paths]))
+                transitive_data.append(build_info.compile_data)
         else:
             fail("rust targets can only depend on rust_library, rust_*_library or cc_library " +
                  "targets.")
@@ -470,14 +471,12 @@ def get_linker_and_args(ctx, attr, crate_type, cc_toolchain, feature_configurati
 def _process_build_scripts(
         build_info,
         dep_info,
-        compile_inputs,
         include_link_flags = True):
     """Gathers the outputs from a target's `cargo_build_script` action.
 
     Args:
         build_info (BuildInfo): The target Build's dependency info.
         dep_info (DepInfo): The Depinfo provider form the target Crate's set of inputs.
-        compile_inputs (depset): A set of all files that will participate in the build.
         include_link_flags (bool, optional): Whether to include flags like `-l` that instruct the linker to search for a library.
 
     Returns:
@@ -488,8 +487,7 @@ def _process_build_scripts(
             - (depset[File]): All direct and transitive build flags from the current build info.
     """
     extra_inputs, out_dir, build_env_file, build_flags_files = _create_extra_input_args(build_info, dep_info, include_link_flags = include_link_flags)
-    compile_inputs = depset(transitive = [extra_inputs, compile_inputs])
-    return compile_inputs, out_dir, build_env_file, build_flags_files
+    return extra_inputs, out_dir, build_env_file, build_flags_files
 
 def _symlink_for_ambiguous_lib(actions, toolchain, crate_info, lib):
     """Constructs a disambiguating symlink for a library dependency.
@@ -780,13 +778,18 @@ def collect_inputs(
         ],
     )
 
+    build_script_compile_inputs, out_dir, build_env_file, build_flags_files = _process_build_scripts(
+        build_info = build_info,
+        dep_info = dep_info,
+        include_link_flags = include_link_flags,
+    )
+
     # For backwards compatibility, we also check the value of the `rustc_env_files` attribute when
     # `crate_info.rustc_env_files` is not populated.
     build_env_files = crate_info.rustc_env_files if crate_info.rustc_env_files else getattr(files, "rustc_env_files", [])
-    compile_inputs, out_dir, build_env_file, build_flags_files = _process_build_scripts(build_info, dep_info, compile_inputs, include_link_flags = include_link_flags)
     if build_env_file:
         build_env_files = [f for f in build_env_files] + [build_env_file]
-    compile_inputs = depset(build_env_files, transitive = [compile_inputs])
+    compile_inputs = depset(build_env_files, transitive = [build_script_compile_inputs, compile_inputs])
     return compile_inputs, out_dir, build_env_files, build_flags_files, linkstamp_outs, ambiguous_libs
 
 def construct_arguments(
@@ -1731,8 +1734,13 @@ def _create_extra_input_args(build_info, dep_info, include_link_flags = True):
 
         input_depsets.append(build_info.compile_data)
 
+    out_dir_compile_inputs = depset(
+        input_files,
+        transitive = [dep_info.link_search_path_files, dep_info.transitive_data] + input_depsets,
+    )
+
     return (
-        depset(input_files, transitive = [dep_info.link_search_path_files] + input_depsets),
+        out_dir_compile_inputs,
         out_dir,
         build_env_file,
         depset(build_flags_files, transitive = [dep_info.link_search_path_files]),
diff --git a/test/dep_env/BUILD.bazel b/test/dep_env/BUILD.bazel
index 82acfbb7cb..994731efa5 100644
--- a/test/dep_env/BUILD.bazel
+++ b/test/dep_env/BUILD.bazel
@@ -113,4 +113,5 @@ genrule(
     srcs = ["dep_dir"],
     outs = ["set_dep_dir.env"],
     cmd = "echo DEP_DIR=\\$${pwd}/$(execpath dep_dir) > $@",
+    cmd_bat = "echo DEP_DIR=$${pwd}/$(execpath dep_dir) > $@",
 )
diff --git a/test/dep_env/dep_env.bzl b/test/dep_env/dep_env.bzl
index f571fa6266..84f96a3735 100644
--- a/test/dep_env/dep_env.bzl
+++ b/test/dep_env/dep_env.bzl
@@ -1,14 +1,59 @@
-"""Tests for passing configuration to cargo_build_script rules"""
+"""Tests for passing configuration to cargo_dep_env rules"""
 
-def _create_dep_dir(ctx):
-    out = ctx.actions.declare_directory("dep_dir")
-    ctx.actions.run_shell(
+_SH_WRITER = """\
+#!/usr/bin/env bash
+set -euo pipefail
+echo content > $@
+"""
+
+_BAT_WRITER = """\
+@ECHO OFF
+echo content > %*
+"""
+
+def _create_dep_dir_impl(ctx):
+    is_windows = ctx.attr.platform.values()[0] == "windows"
+    writer = ctx.actions.declare_file("{}.writer.{}".format(
+        ctx.label.name,
+        ".bat" if is_windows else ".sh",
+    ))
+    ctx.actions.write(
+        output = writer,
+        content = _BAT_WRITER if is_windows else _SH_WRITER,
+        is_executable = True,
+    )
+
+    out = ctx.actions.declare_directory("{}.dep_dir".format(ctx.label.name))
+    ctx.actions.run(
+        executable = writer,
         outputs = [out],
-        arguments = [out.path],
-        command = 'echo contents > "$@/a_file"',
+        arguments = [
+            "{}\\a_file".format(out.path) if is_windows else "{}/a_file".format(out.path),
+        ],
     )
+
     return [DefaultInfo(files = depset(direct = [out]))]
 
-create_dep_dir = rule(
-    implementation = _create_dep_dir,
+_create_dep_dir = rule(
+    implementation = _create_dep_dir_impl,
+    attrs = {
+        "platform": attr.label_keyed_string_dict(
+            doc = "The name of the exec platform",
+            cfg = "exec",
+            mandatory = True,
+        ),
+    },
 )
+
+def create_dep_dir(name, **kwargs):
+    native.filegroup(
+        name = "{}_".format(name),
+    )
+    _create_dep_dir(
+        name = name,
+        platform = select({
+            "@platforms//os:windows": {":{}_".format(name): "windows"},
+            "//conditions:default": {":{}_".format(name): "unix"},
+        }),
+        **kwargs
+    )
diff --git a/test/dep_env/read_b.rs b/test/dep_env/read_b.rs
index b63db42a03..ad89fdce3d 100644
--- a/test/dep_env/read_b.rs
+++ b/test/dep_env/read_b.rs
@@ -1,5 +1,5 @@
 use std::env::var;
 
 fn main() {
-    assert_eq!(var("DEP_Y_B").unwrap(), "b_value");
+    assert_eq!(var("DEP_Y_B").unwrap().trim(), "b_value");
 }
diff --git a/test/dep_env/read_dep_dir.rs b/test/dep_env/read_dep_dir.rs
index c9a82edef1..a9484bad37 100644
--- a/test/dep_env/read_dep_dir.rs
+++ b/test/dep_env/read_dep_dir.rs
@@ -1,9 +1,18 @@
-use std::{env::var, fs, io::Result};
+use std::env::var;
+use std::fs;
+use std::io::Result;
+use std::path::PathBuf;
 
 fn main() {
-    let dep_dir = &var("DEP_DIR").expect("DEP_DIR should be set");
-    let entries = fs::read_dir(dep_dir)
-        .expect("Failed to open DEP_DIR directory")
+    let dep_dir = PathBuf::from(var("DEP_DIR").expect("DEP_DIR should be set").trim());
+    let entries = fs::read_dir(&dep_dir)
+        .unwrap_or_else(|e| {
+            panic!(
+                "Failed to open DEP_DIR directory: {}\n{:?}",
+                dep_dir.display(),
+                e
+            )
+        })
         .collect::<Result<Vec<_>>>()
         .expect("Failed to read DEP_DIR directory entries");
     let entries = entries
diff --git a/test/toolchain/BUILD.bazel b/test/toolchain/BUILD.bazel
index 6400af931e..bc8e0112ee 100644
--- a/test/toolchain/BUILD.bazel
+++ b/test/toolchain/BUILD.bazel
@@ -9,6 +9,7 @@ genrule(
     # rustc assumes it can read things like librustc_driver in order to run this command.
     # This is a test to ensure we supply all of the files rustc needs as part of the current_rust_toolchain.
     cmd = "$(RUSTC) --print=cfg > $@",
+    cmd_bat = "$(RUSTC) --print=cfg > $@",
     toolchains = ["@rules_rust//rust/toolchain:current_rust_toolchain"],
     tools = ["@rules_rust//rust/toolchain:current_rust_toolchain"],
 )
diff --git a/test/unit/location_expansion/location_expansion_test.bzl b/test/unit/location_expansion/location_expansion_test.bzl
index a58d974980..96b6bf89e8 100644
--- a/test/unit/location_expansion/location_expansion_test.bzl
+++ b/test/unit/location_expansion/location_expansion_test.bzl
@@ -1,6 +1,7 @@
 """Unittest to verify location expansion in rustc flags"""
 
 load("@bazel_skylib//lib:unittest.bzl", "analysistest")
+load("@bazel_skylib//rules:write_file.bzl", "write_file")
 load("//rust:defs.bzl", "rust_library")
 load("//test/unit:common.bzl", "assert_action_mnemonic", "assert_argv_contains")
 
@@ -17,10 +18,14 @@ def _location_expansion_rustc_flags_test(ctx):
 location_expansion_rustc_flags_test = analysistest.make(_location_expansion_rustc_flags_test)
 
 def _location_expansion_test():
-    native.genrule(
+    write_file(
         name = "flag_generator",
-        outs = ["generated_flag.data"],
-        cmd = "echo --cfg=test_flag > $@",
+        out = "generated_flag.data",
+        content = [
+            "--cfg=test_flag",
+            "",
+        ],
+        newline = "unix",
     )
 
     rust_library(
diff --git a/test/unit/pipelined_compilation/wrap.bzl b/test/unit/pipelined_compilation/wrap.bzl
index 09c2a6c737..fb4c6db067 100644
--- a/test/unit/pipelined_compilation/wrap.bzl
+++ b/test/unit/pipelined_compilation/wrap.bzl
@@ -6,21 +6,21 @@ load("//rust/private:providers.bzl", "BuildInfo", "CrateInfo", "DepInfo", "DepVa
 # buildifier: disable=bzl-visibility
 load("//rust/private:rustc.bzl", "rustc_compile_action")
 
-def _wrap_impl(ctx):
-    rs_file = ctx.actions.declare_file(ctx.label.name + "_wrapped.rs")
-    crate_name = ctx.attr.crate_name if ctx.attr.crate_name else ctx.label.name
-    ctx.actions.run_shell(
-        outputs = [rs_file],
-        command = """cat <<EOF > {}
+_CONTENT = """\
 // crate_name: {}
 use to_wrap::to_wrap;
 
 pub fn wrap() {{
     to_wrap();
 }}
-EOF
-""".format(rs_file.path, crate_name),
-        mnemonic = "WriteWrapperRsFile",
+"""
+
+def _wrap_impl(ctx):
+    rs_file = ctx.actions.declare_file(ctx.label.name + "_wrapped.rs")
+    crate_name = ctx.attr.crate_name if ctx.attr.crate_name else ctx.label.name
+    ctx.actions.write(
+        output = rs_file,
+        content = _CONTENT.format(crate_name),
     )
 
     toolchain = ctx.toolchains[Label("//rust:toolchain")]
diff --git a/test/unit/toolchain/subpackage/BUILD.bazel b/test/unit/toolchain/subpackage/BUILD.bazel
index 0c8ace8c97..e8f3d676f1 100644
--- a/test/unit/toolchain/subpackage/BUILD.bazel
+++ b/test/unit/toolchain/subpackage/BUILD.bazel
@@ -1,7 +1,10 @@
-genrule(
+load("@bazel_skylib//rules:write_file.bzl", "write_file")
+
+write_file(
     name = "dummy_rlib",
-    outs = ["core.rlib"],
-    cmd = "touch $@",
+    out = "core.rlib",
+    content = [],
+    newline = "unix",
 )
 
 filegroup(