diff --git a/README.md b/README.md
index 2acff13..31f31b5 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,8 @@
 
 This repository uses [chezmoi](https://www.chezmoi.io/) to deploy regular dotfiles on Windows and Linux. Repository support files stay outside the `home/` source state.
 
+Fresh bootstrap installations keep the Git working tree at `~/.dotfiles`. The generated chezmoi configuration persists that directory, so regular commands such as `chezmoi update` and `chezmoi cd` use it without extra flags. Because `.chezmoiroot` points to `home`, `chezmoi source-path` resolves to `~/.dotfiles/home`. Existing installations are not moved automatically.
+
 ## Quick installation
 
 ### Windows
@@ -42,6 +44,7 @@ For dotfiles plus installer-managed package/application/module updates, use `upd
 
 ## State details
 
+- `home/.chezmoi.toml.tmpl` persists the source directory selected during `chezmoi init`; fresh bootstraps explicitly select `~/.dotfiles`.
 - `home/.chezmoiroot` is represented by the repository-level `.chezmoiroot`, pointing to `home`.
 - Windows-only `.wslconfig` and Linux-only Zsh/Sheldon state are filtered by `home/.chezmoiignore`.
 - `~/.gitconfig.local`, `~/.codex/config.toml`, and `~/.codex/rules/default.rules` use chezmoi create-only semantics and are not overwritten after creation.
diff --git a/bootstrap.cmd b/bootstrap.cmd
index 861aeca..7163445 100644
--- a/bootstrap.cmd
+++ b/bootstrap.cmd
@@ -121,7 +121,7 @@ for /f "delims=" %%R in ('chezmoi.exe source-path 2^>nul') do set "SOURCE_ROOT=%
 if defined SOURCE_ROOT if exist "%SOURCE_ROOT%\.chezmoiroot" goto existing_chezmoi
 if defined SOURCE_ROOT for %%P in ("%SOURCE_ROOT%\..") do if exist "%%~fP\.chezmoiroot" goto existing_chezmoi
 
-chezmoi.exe init "%REPO_URL%"
+chezmoi.exe --source "%USERPROFILE%\.dotfiles" init "%REPO_URL%"
 exit /b %ERRORLEVEL%
 
 :existing_chezmoi
diff --git a/bootstrap.sh b/bootstrap.sh
old mode 100644
new mode 100755
index d57e69b..8d4b579
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -82,7 +82,7 @@ else
     if [[ -f "$SOURCE_ROOT/.chezmoiroot" || -f "$(dirname "$SOURCE_ROOT")/.chezmoiroot" ]]; then
         existing_source=true
     else
-        chezmoi init "$REPO_URL"
+        chezmoi --source "$HOME/.dotfiles" init "$REPO_URL"
     fi
 fi
 
diff --git a/home/.chezmoi.toml.tmpl b/home/.chezmoi.toml.tmpl
new file mode 100644
index 0000000..edbecd8
--- /dev/null
+++ b/home/.chezmoi.toml.tmpl
@@ -0,0 +1 @@
+sourceDir = {{ joinPath .chezmoi.homeDir ".dotfiles" | quote }}
diff --git a/tests/linux/assert-state.sh b/tests/linux/assert-state.sh
old mode 100644
new mode 100755
index c4e0c67..c4bfa04
--- a/tests/linux/assert-state.sh
+++ b/tests/linux/assert-state.sh
@@ -14,6 +14,11 @@ printf 'HOME: %s\n' "$HOME"
 printf 'chezmoi: %s\n' "$(chezmoi --version)"
 printf 'chezmoi source-path: %s\n' "$(chezmoi source-path)"
 
+source_path="$(chezmoi source-path)"
+working_tree="$(chezmoi execute-template '{{ .chezmoi.workingTree }}')"
+[[ "$working_tree" == "$HOME/.dotfiles" ]] || fail "chezmoi working tree is $working_tree, expected $HOME/.dotfiles"
+[[ "$source_path" == "$HOME/.dotfiles/home" ]] || fail "chezmoi source path is $source_path, expected $HOME/.dotfiles/home"
+
 case "$expected_distro" in
     debian) [[ -f /etc/debian_version ]] || fail "Debian detection marker is missing" ;;
     arch) [[ -f /etc/arch-release ]] || fail "Arch detection marker is missing" ;;
diff --git a/tests/static/validate-architecture.py b/tests/static/validate-architecture.py
old mode 100644
new mode 100755
index 19da9f6..31dd57b
--- a/tests/static/validate-architecture.py
+++ b/tests/static/validate-architecture.py
@@ -33,6 +33,7 @@ def read_text(path: str) -> str:
     fail(".chezmoiroot must contain 'home'")
 
 required_paths = (
+    "home/.chezmoi.toml.tmpl",
     "home",
     "scripts/linux/packages-debian.txt",
     "scripts/linux/cleanup-broken-managed-links.sh",
diff --git a/tests/windows/assert-allsigned.ps1 b/tests/windows/assert-allsigned.ps1
index 274c408..60052ac 100644
--- a/tests/windows/assert-allsigned.ps1
+++ b/tests/windows/assert-allsigned.ps1
@@ -211,6 +211,17 @@ function Assert-CleanChezMoi {
 
 $sourcePath = ((Invoke-Chezmoi @("source-path")) -join "").Trim()
 Write-Host "chezmoi source-path: $sourcePath"
+$expectedWorkingTree = [IO.Path]::GetFullPath((Join-Path $HOME ".dotfiles")).TrimEnd([IO.Path]::DirectorySeparatorChar)
+$workingTree = ((Invoke-Chezmoi @("execute-template", "{{ .chezmoi.workingTree }}")) -join "").Trim()
+$actualWorkingTree = [IO.Path]::GetFullPath($workingTree).TrimEnd([IO.Path]::DirectorySeparatorChar)
+if (-not $actualWorkingTree.Equals($expectedWorkingTree, [StringComparison]::OrdinalIgnoreCase)) {
+    Fail "chezmoi working tree is $actualWorkingTree, expected $expectedWorkingTree"
+}
+$expectedSourcePath = [IO.Path]::GetFullPath((Join-Path $expectedWorkingTree "home")).TrimEnd([IO.Path]::DirectorySeparatorChar)
+$actualSourcePath = [IO.Path]::GetFullPath($sourcePath).TrimEnd([IO.Path]::DirectorySeparatorChar)
+if (-not $actualSourcePath.Equals($expectedSourcePath, [StringComparison]::OrdinalIgnoreCase)) {
+    Fail "chezmoi source path is $actualSourcePath, expected $expectedSourcePath"
+}
 $managedAppsPath = Join-Path $RepoRoot "scripts\windows\managed-apps.csv"
 $coreApps = @(Import-Csv -LiteralPath $managedAppsPath | Where-Object Category -eq "core")
 foreach ($app in $coreApps) {
diff --git a/tests/windows/assert-state.ps1 b/tests/windows/assert-state.ps1
index f68d1e9..e3813aa 100644
--- a/tests/windows/assert-state.ps1
+++ b/tests/windows/assert-state.ps1
@@ -41,6 +41,18 @@ $sourcePath = ((Invoke-Chezmoi @("source-path")) -join "").Trim()
 Write-Host "chezmoi source-path: $sourcePath"
 if (-not (Test-Path -LiteralPath $sourcePath)) { Fail "chezmoi source path does not exist: $sourcePath" }
 
+$expectedWorkingTree = [IO.Path]::GetFullPath((Join-Path $HOME ".dotfiles")).TrimEnd([IO.Path]::DirectorySeparatorChar)
+$workingTree = ((Invoke-Chezmoi @("execute-template", "{{ .chezmoi.workingTree }}")) -join "").Trim()
+$actualWorkingTree = [IO.Path]::GetFullPath($workingTree).TrimEnd([IO.Path]::DirectorySeparatorChar)
+if (-not $actualWorkingTree.Equals($expectedWorkingTree, [StringComparison]::OrdinalIgnoreCase)) {
+    Fail "chezmoi working tree is $actualWorkingTree, expected $expectedWorkingTree"
+}
+$expectedSourcePath = [IO.Path]::GetFullPath((Join-Path $expectedWorkingTree "home")).TrimEnd([IO.Path]::DirectorySeparatorChar)
+$actualSourcePath = [IO.Path]::GetFullPath($sourcePath).TrimEnd([IO.Path]::DirectorySeparatorChar)
+if (-not $actualSourcePath.Equals($expectedSourcePath, [StringComparison]::OrdinalIgnoreCase)) {
+    Fail "chezmoi source path is $actualSourcePath, expected $expectedSourcePath"
+}
+
 $requiredFiles = @(
     (Join-Path $HOME ".gitconfig"),
     (Join-Path $HOME ".gitconfig.local"),