diff --git a/.gitignore b/.gitignore
index b46a1ca2..ad990c37 100644
--- a/.gitignore
+++ b/.gitignore
@@ -36,6 +36,8 @@ install-sh
 missing
 stamp-h1
 .dirstamp
+linux/
+windows/
 
 # objects
 snapraid
diff --git a/AGENTS.md b/AGENTS.md
index 6e03126a..fa018762 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -80,12 +80,16 @@ SnapRAID is designed to recover from an interruption, including `SIGKILL`, at an
 - `Makefile.am`: Source file lists, dependencies, install hooks (including rules for generating documentation)
 - `uncrustify.cfg`: Code formatting rules for main application source files
 - `linux.cfg`: Code formatting rules for `raid/` directory and its subdirectories
-- Run `make doc` to regenerate all manual pages (`*.1`) and text manuals (`*.txt`)
+- Run `(cd linux && make doc)` to regenerate all manual pages (`*.1`) and text manuals (`*.txt`)
 - Always use parallel compilation with `make -j$(nproc)` instead of plain `make`
 - Create temporary files and directories under `/tmp/snapraid/`.
-- To cross-compile for Windows x64: build out-of-tree in `/tmp/snapraid/` so the Linux configuration is preserved:
-  `mkdir -p /tmp/snapraid/windows && (cd /tmp/snapraid/windows && /path/to/configure.windows-x64 && make -j$(nproc))`
-  Subsequent Windows rebuilds only require: `(cd /tmp/snapraid/windows && make -j$(nproc))`
+- Both Linux and Windows builds are out-of-tree in dedicated subdirectories (`linux/` and `windows/`) in the project directory, keeping the root directory clean:
+  - Linux build:
+    `mkdir -p linux && (cd linux && ../configure && make -j$(nproc))`
+    Subsequent Linux rebuilds: `(cd linux && make -j$(nproc))`
+  - Windows x64 cross-compilation:
+    `mkdir -p windows && (cd windows && ../configure.windows-x64 && make -j$(nproc))`
+    Subsequent Windows rebuilds: `(cd windows && make -j$(nproc))`
 - The Windows build needs to be tested only when modifying Windows-specific code (e.g., `os/mingw.*`, `cmdline/mingwapp.c`, or Windows-specific `#ifdef` paths)
 
 ## Code Style Guidelines
@@ -137,8 +141,8 @@ SnapRAID is designed to recover from an interruption, including `SIGKILL`, at an
 #### Testing Changes
 
 - Never run `make check` because it's too expansive
-- Run `./snapraid test` for the regression test
-- The `test` and `selftest` suites (in `cmdline/selftest.c` and `./snapraid test`) must be strictly memory-only without creating files or performing filesystem I/O
-- If running the speed benchmark (`./snapraid -T`), always use `--speed-test-period 100` (e.g. `./snapraid -T --speed-test-period 100`) to run it faster
+- Run `./linux/snapraid test` for the regression test
+- The `test` and `selftest` suites (in `cmdline/selftest.c` and `./linux/snapraid test`) must be strictly memory-only without creating files or performing filesystem I/O
+- If running the speed benchmark (`./linux/snapraid -T`), always use `--speed-test-period 100` (e.g. `./linux/snapraid -T --speed-test-period 100`) to run it faster
 - The Windows build needs to be tested only when modifying Windows-specific code
 - Verify error paths and recovery scenarios (the test suite covers aborted sync, UUID changes, disk failures)
diff --git a/GNUmakefile b/GNUmakefile
new file mode 100644
index 00000000..e84f6b87
--- /dev/null
+++ b/GNUmakefile
@@ -0,0 +1,18 @@
+# If Makefile exists (generated by ./configure in this directory), delegate
+# directly to it so that in-tree builds work normally as if this file were absent.
+# Otherwise, redirect all targets to linux/Makefile for out-of-tree builds.
+# Named GNUmakefile so it takes precedence in GNU Make without conflicting with
+# Makefile on case-insensitive filesystems (Windows/macOS).
+ifeq ($(wildcard Makefile),Makefile)
+include Makefile
+else ifeq ($(wildcard linux/Makefile),linux/Makefile)
+all doc:
+	$(MAKE) -C linux $@
+
+.DEFAULT:
+	$(MAKE) -C linux $@
+
+.PHONY: all doc
+else
+$(error SnapRAID is not configured. Run './configure')
+endif
diff --git a/configure.analyzer b/configure.analyzer
index 68cb0dc5..97f53575 100755
--- a/configure.analyzer
+++ b/configure.analyzer
@@ -1 +1,3 @@
-./configure CC=/usr/libexec/ccc-analyzer
+DIR=$(dirname "$0")
+"$DIR/configure" CC=/usr/libexec/ccc-analyzer
+
diff --git a/configure.windows-x64 b/configure.windows-x64
index 3e413824..ba330db5 100755
--- a/configure.windows-x64
+++ b/configure.windows-x64
@@ -1,35 +1,2 @@
-#!/bin/bash
-
-# Identify the original source directory
 DIR=$(dirname "$0")
-# Resolve the absolute path of the source directory to prevent path ambiguity
-SRC_DIR=$(cd "$DIR" && pwd)
-
-# List of critical Autotools files to hide temporarily
-FILES_TO_HIDE=("config.status" "Makefile" "config.log")
-HIDDEN_FILES=()
-
-# Function to restore original files when the script finishes or exits
-restore_files() {
-    for file in "${HIDDEN_FILES[@]}"; do
-        if [ -f "$SRC_DIR/${file}.bak" ]; then
-            mv "$SRC_DIR/${file}.bak" "$SRC_DIR/$file"
-        fi
-    done
-}
-
-# Ensure files are restored under any exit condition (success, error, or interruption like Ctrl+C)
-trap restore_files EXIT INT TERM
-
-# 1. Mask the files in the original source directory
-for file in "${FILES_TO_HIDE[@]}"; do
-    if [ -f "$SRC_DIR/$file" ]; then
-        mv "$SRC_DIR/$file" "$SRC_DIR/${file}.bak"
-        HIDDEN_FILES+=("$file") # Keep track of files that were actually renamed
-    fi
-done
-
-# 2. Run the original configure command
-"$SRC_DIR/configure" --host=x86_64-w64-mingw32.static --build=$("$SRC_DIR/config.guess") "$@"
-
-# Note: The 'restore_files' function will automatically trigger here via the trap hook.
+"$DIR/configure" --host=x86_64-w64-mingw32.static --build=$("$DIR/config.guess") "$@"
diff --git a/makedist.sh b/makedist.sh
index e54d7c2d..b10f9a2e 100755
--- a/makedist.sh
+++ b/makedist.sh
@@ -47,3 +47,6 @@ sudo sh makeslackware.sh
 sudo sh makearch.sh
 sudo sh makedeb.sh
 sudo sh makerpm.sh
+
+make distclean
+