diff --git a/Cargo.lock b/Cargo.lock
index fcd7d806843..d3b54343499 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -96,6 +96,16 @@ version = "1.0.87"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "10f00e1f6e58a40e807377c75c6a7f97bf9044fab57816f2414e6f5f4499d7b8"
 
+[[package]]
+name = "argfile"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0a1cc0ba69de57db40674c66f7cf2caee3981ddef084388482c95c0e2133e5e8"
+dependencies = [
+ "fs-err",
+ "os_str_bytes",
+]
+
 [[package]]
 name = "arrayvec"
 version = "0.7.6"
@@ -360,6 +370,7 @@ name = "codeql-rust"
 version = "0.1.0"
 dependencies = [
  "anyhow",
+ "argfile",
  "clap",
  "codeql-extractor",
  "figment",
@@ -374,6 +385,7 @@ dependencies = [
  "ra_ap_project_model",
  "ra_ap_syntax",
  "ra_ap_vfs",
+ "rust-extractor-macros",
  "serde",
  "serde_with",
  "stderrlog",
@@ -643,6 +655,15 @@ version = "1.0.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
 
+[[package]]
+name = "fs-err"
+version = "2.11.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "88a41f105fe1d5b6b34b2055e3dc59bb79b46b48b2040b9e6c7b4b5de097aa41"
+dependencies = [
+ "autocfg",
+]
+
 [[package]]
 name = "fsevent-sys"
 version = "4.1.0"
@@ -1064,6 +1085,15 @@ version = "11.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b410bbe7e14ab526a0e86877eb47c6996a2bd7746f027ba551028c925390e4e9"
 
+[[package]]
+name = "os_str_bytes"
+version = "7.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7ac44c994af577c799b1b4bd80dc214701e349873ad894d6cdf96f4f7526e0b9"
+dependencies = [
+ "memchr",
+]
+
 [[package]]
 name = "overload"
 version = "0.1.1"
@@ -1875,6 +1905,14 @@ dependencies = [
  "text-size",
 ]
 
+[[package]]
+name = "rust-extractor-macros"
+version = "0.1.0"
+dependencies = [
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "rustc-hash"
 version = "1.1.0"
diff --git a/Cargo.toml b/Cargo.toml
index 5f095736c8a..4aacef79adc 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -6,6 +6,7 @@ members = [
     "shared/tree-sitter-extractor",
     "ruby/extractor",
     "rust/extractor",
+    "rust/extractor/macros",
 ]
 
 [patch.crates-io]
diff --git a/rust/extractor/Cargo.toml b/rust/extractor/Cargo.toml
index c849ea4aa46..3b474f90f98 100644
--- a/rust/extractor/Cargo.toml
+++ b/rust/extractor/Cargo.toml
@@ -22,7 +22,6 @@ serde = "1.0.209"
 serde_with = "3.9.0"
 stderrlog = "0.6.0"
 triomphe = "0.1.13"
-# Ideally, we'd like to pull this in via a relative path.
-# However, our bazel/rust tooling chokes on this, c.f. https://github.com/bazelbuild/rules_rust/issues/1525
-# Therefore, we have a pretty bad hack in place instead, see README.md in the codeql-extractor-fake-crate directory.
+argfile = "0.2.1"
 codeql-extractor = { path = "../../shared/tree-sitter-extractor" }
+rust-extractor-macros = { path = "macros" }
diff --git a/rust/extractor/macros/Cargo.toml b/rust/extractor/macros/Cargo.toml
new file mode 100644
index 00000000000..d4d10bc3bde
--- /dev/null
+++ b/rust/extractor/macros/Cargo.toml
@@ -0,0 +1,11 @@
+[package]
+name = "rust-extractor-macros"
+version = "0.1.0"
+edition = "2021"
+
+[lib]
+proc-macro = true
+
+[dependencies]
+quote = "1.0.37"
+syn = { version = "2.0.77", features = ["full"] }
diff --git a/rust/extractor/macros/src/lib.rs b/rust/extractor/macros/src/lib.rs
new file mode 100644
index 00000000000..13472665454
--- /dev/null
+++ b/rust/extractor/macros/src/lib.rs
@@ -0,0 +1,52 @@
+use proc_macro::TokenStream;
+use quote::{quote, format_ident};
+use syn;
+
+
+/// Allow all fields in the extractor config to be also overrideable by extractor CLI flags
+#[proc_macro_attribute]
+pub fn extractor_cli_config(_attr: TokenStream, item: TokenStream) -> TokenStream {
+    let ast = syn::parse_macro_input!(item as syn::ItemStruct);
+    let name = &ast.ident;
+    let new_name = format_ident!("Cli{}", name);
+    let fields: Vec<_> = ast.fields.iter().map(|f| {
+        let id = f.ident.as_ref().unwrap();
+        let ty = &f.ty;
+        if let syn::Type::Path(p) = ty {
+            if p.path.is_ident(&format_ident!("bool")) {
+                return quote! {
+                    #[arg(long)]
+                    #id: bool,
+                };
+            }
+        }
+        if id == &format_ident!("verbose") {
+            quote! {
+                #[arg(long, short, action=clap::ArgAction::Count)]
+                #id: u8,
+            }
+        } else if id == &format_ident!("inputs") {
+            quote! {
+                #id: #ty,
+            }
+        } else {
+            quote! {
+                #[arg(long)]
+                #id: Option<#ty>,
+            }
+        }
+    }).collect();
+    let gen = quote! {
+        #[serde_with::apply(_ => #[serde(default)])]
+        #[derive(Debug, Deserialize, Default)]
+        #ast
+
+        #[serde_with::skip_serializing_none]
+        #[derive(clap::Parser, Serialize)]
+        #[command(about, long_about = None)]
+        struct #new_name {
+            #(#fields)*
+        }
+    };
+    gen.into()
+}
diff --git a/rust/extractor/src/config.rs b/rust/extractor/src/config.rs
index 399c2bb9e7e..310ca2c3649 100644
--- a/rust/extractor/src/config.rs
+++ b/rust/extractor/src/config.rs
@@ -1,14 +1,15 @@
 use anyhow::Context;
-use clap::{ArgAction, Parser, ValueEnum};
+use clap::Parser;
 use codeql_extractor::trap;
 use figment::{
     providers::{Env, Serialized},
     Figment,
 };
+use rust_extractor_macros::extractor_cli_config;
 use serde::{Deserialize, Serialize};
 use std::path::PathBuf;
 
-#[derive(Debug, PartialEq, Eq, Default, Serialize, Deserialize, Clone, Copy, ValueEnum)]
+#[derive(Debug, PartialEq, Eq, Default, Serialize, Deserialize, Clone, Copy, clap::ValueEnum)]
 #[serde(rename_all = "lowercase")]
 #[clap(rename_all = "lowercase")]
 pub enum Compression {
@@ -26,8 +27,7 @@ impl From<Compression> for trap::Compression {
     }
 }
 
-#[serde_with::apply(_ => #[serde(default)])]
-#[derive(Debug, Deserialize, Default)]
+#[extractor_cli_config]
 pub struct Config {
     pub scratch_dir: PathBuf,
     pub trap_dir: PathBuf,
@@ -38,39 +38,10 @@ pub struct Config {
     pub inputs: Vec<PathBuf>,
 }
 
-#[serde_with::apply(_ => #[serde(skip_serializing_if = "is_default")])]
-#[derive(clap::Parser, Serialize)]
-#[command(about, long_about = None)]
-struct CliArgs {
-    #[arg(long)]
-    scratch_dir: Option<PathBuf>,
-    #[arg(long)]
-    trap_dir: Option<PathBuf>,
-    #[arg(long)]
-    source_archive_dir: Option<PathBuf>,
-    #[arg(long)]
-    compression: Option<Compression>,
-    #[arg(short, long, action = ArgAction::Count)]
-    verbose: u8,
-    #[arg(long)]
-    inputs_file: Option<PathBuf>,
-
-    inputs: Vec<PathBuf>,
-}
-
-fn is_default<T: Default + PartialEq>(t: &T) -> bool {
-    *t == Default::default()
-}
-
 impl Config {
     pub fn extract() -> anyhow::Result<Config> {
-        let mut cli_args = CliArgs::parse();
-        if let Some(inputs_file) = cli_args.inputs_file.take() {
-            let inputs_list = std::fs::read_to_string(inputs_file).context("reading file list")?;
-            cli_args
-                .inputs
-                .extend(inputs_list.split_terminator("\n").map(PathBuf::from));
-        }
+        let args = argfile::expand_args(argfile::parse_fromfile, argfile::PREFIX)?;
+        let cli_args = CliConfig::parse_from(args);
         Figment::new()
             .merge(Env::prefixed("CODEQL_EXTRACTOR_RUST_"))
             .merge(Env::prefixed("CODEQL_EXTRACTOR_RUST_OPTION_"))
diff --git a/rust/tools/index-files.sh b/rust/tools/index-files.sh
index da4b841b692..f3d93fbaf4a 100755
--- a/rust/tools/index-files.sh
+++ b/rust/tools/index-files.sh
@@ -2,4 +2,4 @@
 
 set -eu
 
-exec "$CODEQL_EXTRACTOR_RUST_ROOT/tools/$CODEQL_PLATFORM/extractor" --inputs-file="$1"
+exec "$CODEQL_EXTRACTOR_RUST_ROOT/tools/$CODEQL_PLATFORM/extractor" @"$1"