diff --git a/Cargo.lock b/Cargo.lock
index f7c0905f54..8b259556ee 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -152,22 +152,6 @@ dependencies = [
  "serde_json",
 ]
 
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- "predicates-core",
- "predicates-tree",
- "wait-timeout",
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-
 [[package]]
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@@ -490,17 +474,6 @@ dependencies = [
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- "serde",
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-
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@@ -684,20 +657,6 @@ dependencies = [
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 ]
 
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- "tempfile",
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-
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@@ -829,12 +788,6 @@ dependencies = [
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 checksum = "212d0f5754cb6769937f4501cc0e67f4f4483c8d2c3e1e922ee9edbe4ab4c7c0"
 
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-
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 checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
 
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diff --git a/Cargo.toml b/Cargo.toml
index 72b167a3d4..9a10754af7 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -11,7 +11,9 @@ members = [
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     "stacks-signer",
     "stacks-node",
-    "contrib/tools/config-docs-generator"]
+]
+
+exclude = ["contrib/tools/config-docs-generator"]
 
 # Dependencies we want to keep the same between workspace members
 [workspace.dependencies]
diff --git a/contrib/tools/config-docs-generator/Cargo.lock b/contrib/tools/config-docs-generator/Cargo.lock
new file mode 100644
index 0000000000..fb511e43a1
--- /dev/null
+++ b/contrib/tools/config-docs-generator/Cargo.lock
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diff --git a/contrib/tools/config-docs-generator/Cargo.toml b/contrib/tools/config-docs-generator/Cargo.toml
index ccf1cdbb80..d1171a3993 100644
--- a/contrib/tools/config-docs-generator/Cargo.toml
+++ b/contrib/tools/config-docs-generator/Cargo.toml
@@ -17,14 +17,14 @@ name = "integration"
 path = "tests/integration.rs"
 
 [dependencies]
-serde = { version = "1.0", features = ["derive"] }
-serde_json = "1.0"
-clap = { version = "4.0", features = ["derive"] }
-regex = "1.0"
-anyhow = "1.0"
-once_cell = "1.18"
+serde = { version = "1.0.219", default-features=false, features = ["derive"] }
+serde_json = { version = "1.0.142", default-features = false, features = ["std"] }
+clap = { version = "4.5.44", features = ["derive"] }
+regex = { version = "1.11.1", default-features = false }
+anyhow = { version = "1.0.99", default-features = false, features = ["std"] }
+once_cell = { version = "1.21.3", default-features = false, features = ["std"] }
 
 # Add test dependencies
 [dev-dependencies]
-tempfile = "3.0"
-assert_cmd = "2.0"
+tempfile = { version = "3.20.0", default-features = false }
+assert_cmd = { version = "2.0.17", default-features = false }
diff --git a/contrib/tools/config-docs-generator/generate-config-docs.sh b/contrib/tools/config-docs-generator/generate-config-docs.sh
index dea9459ac1..8725ffe03d 100755
--- a/contrib/tools/config-docs-generator/generate-config-docs.sh
+++ b/contrib/tools/config-docs-generator/generate-config-docs.sh
@@ -55,7 +55,8 @@ main() {
     mkdir -p "$(dirname "$OUTPUT_FILE")"
     mkdir -p "$TEMP_DIR"
 
-    cd "$PROJECT_ROOT"
+    # Move to the script's directory to build `config-docs-generator`
+    cd "$SCRIPT_DIR"
 
     # Step 1: Build the documentation generation tools
     if [[ "$SKIP_BUILD" != "true" ]]; then
@@ -74,6 +75,9 @@ main() {
     fi
     log_info "Structs to be documented: $TARGET_STRUCTS"
 
+    # Move to the project's workspace root to run the extract-docs binary
+    cd "$PROJECT_ROOT"
+
     "$EXTRACT_DOCS_BIN" \
         --package stackslib \
         --structs "$TARGET_STRUCTS" \