diff --git a/README.md b/README.md
index a7265f8..98f7934 100644
--- a/README.md
+++ b/README.md
@@ -100,28 +100,67 @@ powershell -ExecutionPolicy Bypass -File .\scripts\reinstall.ps1
 
 Or from the tray menu: **Reinstall**.
 
-### Running without installing
+### Run from source (no install required)
 
 ```powershell
 # Activate the venv first
 .venv\Scripts\Activate.ps1
 
-# Then run directly
+# Start the tray
 python -m selfsnap tray
+
+# Take a manual capture
 python -m selfsnap capture --trigger manual
+
+# Run a scheduled capture for a specific schedule
+python -m selfsnap capture --trigger scheduled --schedule-id morning
+
+# Sync Windows Task Scheduler tasks from config
+python -m selfsnap sync-scheduler
+
+# Catch up missed schedule slots (run on startup to reconcile gaps)
+python -m selfsnap reconcile
+
+# Run diagnostics
+python -m selfsnap doctor
+python -m selfsnap diag
+
+# Print the installed version
+python -m selfsnap --version
 ```
 
-### Start the tray (after install)
+### Run after install
+
+Once `install.ps1` has been run, the `SelfSnap` wrapper is on your `PATH`:
 
 ```powershell
+# Start the tray
 SelfSnap tray
-```
 
-### Run diagnostics
+# Take a manual capture
+SelfSnap capture --trigger manual
 
-```powershell
+# Run a scheduled capture
+SelfSnap capture --trigger scheduled --schedule-id morning
+
+# Sync Task Scheduler
+SelfSnap sync-scheduler
+
+# Reconcile missed slots
+SelfSnap reconcile
+
+# Diagnostics
 SelfSnap doctor
 SelfSnap diag
+
+# Check for updates without installing
+SelfSnap update --check-only
+
+# Reinstall from current checkout
+SelfSnap reinstall
+
+# Uninstall (prompts for confirmation)
+SelfSnap uninstall
 ```
 
 ## Runtime storage
@@ -206,33 +245,6 @@ If you are using the current source checkout rather than reading historical desi
 - `docs/CONFIG_REFERENCE.md`
 - `docs/WORKFLOWS.md`
 
-## Commands
-
-```powershell
-selfsnap tray
-selfsnap capture --trigger manual
-selfsnap capture --trigger scheduled --schedule-id morning
-selfsnap reconcile
-selfsnap sync-scheduler
-selfsnap reinstall [--relaunch-tray]
-selfsnap uninstall [--remove-user-data] [--yes]
-selfsnap update    [--check-only] [--relaunch-tray]
-selfsnap diag
-selfsnap doctor
-```
-
-`reinstall`, `uninstall`, and `update` mirror the tray menu actions but are usable from any terminal — useful when the tray is not running or for scripted management.
-
-- `selfsnap update --check-only` prints whether a newer release is available without installing anything.
-- `selfsnap uninstall` prompts `Uninstall SelfSnap? [y/N]` unless `--yes` is passed.
-
-If `scripts/install.ps1` has been run, the wrapper command is:
-
-```powershell
-$env:LOCALAPPDATA\SelfSnap\bin\SelfSnap.cmd tray
-$env:LOCALAPPDATA\SelfSnap\bin\SelfSnap.cmd capture --trigger manual
-```
-
 ## Report Issue
 
 - `Report Issue` is available from the tray menu and is the default tray action where the Windows shell supports pystray default activation.
@@ -353,17 +365,30 @@ mypy src
 
 Pytest temp directories are intentionally kept out of the repo under `%LOCALAPPDATA%\SelfSnap\pytest\tmp`, and the pytest cache provider is disabled to avoid `.pytest_cache` and `pytest-cache-files-*` clutter in the workspace.
 
-If `.pytest_tmp` or `.pytest-work` still exist in the repo root with old timestamps, treat them as legacy leftovers from earlier runs. Current pytest configuration should not recreate them.
+Use `scripts/cleanup_repo_artifacts.ps1` to remove all local artifact and cache folders. It covers:
 
-If stale pytest artifact folders remain from older runs and normal deletion fails, use the dedicated cleanup script:
+- Coverage data: `cov_annotate/`, `.coverage`, `coverage.xml`
+- Bytecode caches: `__pycache__/` (recursive), `*.pyc` / `*.pyo` / `*.pyd`
+- Test caches: `.pytest_cache/`, `.pytest_tmp/`, `.pytest-work/`, `pytest-cache-files-*/`
+- Tool caches: `.ruff_cache/`, `.mypy_cache/`, `.hypothesis/`, `.uv-cache/`
+- Build outputs: `build/`, `dist/`, `*.egg-info/`
+- Any other git-ignored or untracked file
+
+`.venv/` and `.git/` are always protected.
 
 ```powershell
-powershell -ExecutionPolicy Bypass -File .\scripts\cleanup_pytest_artifacts.ps1 -ListOnly
-powershell -ExecutionPolicy Bypass -File .\scripts\cleanup_pytest_artifacts.ps1
-powershell -ExecutionPolicy Bypass -File .\scripts\cleanup_pytest_artifacts.ps1 -RepairAcl
-```
+# Preview what would be removed
+powershell -ExecutionPolicy Bypass -File .\scripts\cleanup_repo_artifacts.ps1 -ListOnly
 
-`-RepairAcl` attempts a UAC-elevated ownership repair for legacy ACL-poisoned folders. Add `-IncludeLocalAppData` only if you also want to remove `%LOCALAPPDATA%\SelfSnap\pytest`.
+# Remove all artifacts
+powershell -ExecutionPolicy Bypass -File .\scripts\cleanup_repo_artifacts.ps1
+
+# Attempt ACL repair (relaunches elevated via UAC), then remove
+powershell -ExecutionPolicy Bypass -File .\scripts\cleanup_repo_artifacts.ps1 -RepairAcl
+
+# Exclude specific paths from removal
+powershell -ExecutionPolicy Bypass -File .\scripts\cleanup_repo_artifacts.ps1 -Exclude ".coverage","coverage.xml"
+```
 
 The setup script prefers a uv-managed Python 3.12 interpreter when `uv` is installed, then falls back to a normal `python` or `py` launcher on PATH. If you need to force a specific interpreter, pass it explicitly:
 
diff --git a/scripts/cleanup_repo_artifacts.ps1 b/scripts/cleanup_repo_artifacts.ps1
new file mode 100644
index 0000000..465ec1a
--- /dev/null
+++ b/scripts/cleanup_repo_artifacts.ps1
@@ -0,0 +1,248 @@
+param(
+    [switch]$ListOnly,
+    [switch]$RepairAcl,
+    [string[]]$Exclude = @(),
+    [switch]$RelaunchedElevated
+)
+
+$ErrorActionPreference = "Stop"
+$PSNativeCommandUseErrorActionPreference = $true
+
+$repoRoot = (Resolve-Path (Join-Path $PSScriptRoot "..")).Path
+
+function Test-Administrator {
+    $identity  = [Security.Principal.WindowsIdentity]::GetCurrent()
+    $principal = [Security.Principal.WindowsPrincipal]::new($identity)
+    return $principal.IsInRole([Security.Principal.WindowsBuiltInRole]::Administrator)
+}
+
+function Get-RelaunchArgumentList {
+    $arguments = @(
+        "-NoProfile",
+        "-ExecutionPolicy", "Bypass",
+        "-File", $PSCommandPath
+    )
+    if ($RepairAcl)  { $arguments += "-RepairAcl" }
+    if ($ListOnly)   { $arguments += "-ListOnly" }
+    if ($Exclude.Count -gt 0) { $arguments += "-Exclude"; $arguments += $Exclude }
+    $arguments += "-RelaunchedElevated"
+    return $arguments
+}
+
+# ── What this script removes ─────────────────────────────────────────────────
+#
+#  Via git status (ignored + untracked):
+#    .pytest_cache/, .pytest_tmp/, .pytest-work/, pytest-cache-files-*/
+#    .ruff_cache/, .mypy_cache/, .hypothesis/
+#    .coverage, coverage.xml, cov_annotate/
+#    __pycache__/, *.pyc, *.pyo, *.pyd, pytest*.out
+#    build/, dist/, *.egg-info/, .uv-cache/, tmp/, artifacts/
+#    and any other git-ignored or untracked item
+#
+#  Via explicit sweep (catches files that may be committed/tracked by git):
+#    cov_annotate/, .coverage, coverage.xml
+#
+#  Via recursive directory sweep under the repo tree:
+#    __pycache__, .pytest_cache, .pytest_tmp, .pytest-work
+#    .ruff_cache, .mypy_cache, .hypothesis, .uv-cache, *.egg-info
+#
+#  Via recursive file sweep:
+#    *.pyc, *.pyo, *.pyd, pytest*.out
+#
+# Protected (never removed even if gitignored):
+#    .venv/, venv/, .git/
+#
+# ─────────────────────────────────────────────────────────────────────────────
+
+# Directories that are always protected — never removed even if gitignored.
+$ProtectedTopLevel = [System.Collections.Generic.HashSet[string]]::new(
+    [string[]]@('.venv', 'venv', '.git'),
+    [StringComparer]::OrdinalIgnoreCase
+)
+
+# Explicit paths relative to repo root that are targeted even when tracked by git.
+$ExplicitPaths = @(
+    'cov_annotate'
+    '.coverage'
+    'coverage.xml'
+)
+
+# Directory names removed recursively anywhere in the tree.
+$RecursiveDirNames = @(
+    '__pycache__'
+    '.pytest_cache'
+    '.pytest_tmp'
+    '.pytest-work'
+    '.ruff_cache'
+    '.mypy_cache'
+    '.hypothesis'
+    '.uv-cache'
+)
+
+# File patterns removed recursively anywhere in the tree.
+$RecursiveFilePatterns = @(
+    '*.pyc'
+    '*.pyo'
+    '*.pyd'
+    'pytest*.out'
+)
+
+# ── Candidate collection ──────────────────────────────────────────────────────
+
+function Get-ArtifactCandidates {
+    param([string]$RepoRoot, [string[]]$ExcludeList)
+
+    $seen       = [System.Collections.Generic.HashSet[string]]::new([StringComparer]::OrdinalIgnoreCase)
+    $candidates = [System.Collections.Generic.List[object]]::new()
+
+    function Add-Candidate {
+        param([string]$FullPath, [string]$Label)
+        if (-not (Test-Path -LiteralPath $FullPath)) { return }
+        $relPath = $FullPath.Substring($RepoRoot.Length).TrimStart('\').TrimEnd('\')
+        if ([string]::IsNullOrWhiteSpace($relPath)) { return }
+        $topLevel = $relPath.Split('\')[0]
+        if ($ProtectedTopLevel.Contains($topLevel)) { return }
+        if ($ExcludeList -contains $relPath) { return }
+        if (-not $seen.Add($relPath)) { return }
+        $item = Get-Item -LiteralPath $FullPath -Force
+        $candidates.Add([pscustomobject]@{
+            RelativePath = $relPath
+            FullPath     = $item.FullName
+            IsDirectory  = $item.PSIsContainer
+            Label        = $Label
+        })
+    }
+
+    # Pass 1: git status — ignored (!!) and untracked (??)
+    $gitLines = & git -C $RepoRoot status --porcelain=v1 --ignored --untracked-files=all 2>&1
+    foreach ($line in $gitLines) {
+        if ($line.Length -lt 4) { continue }
+        $code = $line.Substring(0, 2)
+        if ($code -ne '!!' -and $code -ne '??') { continue }
+        # git quotes paths that contain spaces or special characters — strip those quotes
+        $rel  = $line.Substring(3).Trim().Trim('"').TrimEnd('/').Replace('/', '\')
+        $lbl  = if ($code -eq '!!') { 'git-ignored' } else { 'untracked' }
+        Add-Candidate -FullPath (Join-Path $RepoRoot $rel) -Label $lbl
+    }
+
+    # Pass 2: explicit known artifacts (catches committed files like coverage.xml)
+    foreach ($rel in $ExplicitPaths) {
+        Add-Candidate -FullPath (Join-Path $RepoRoot $rel) -Label 'explicit'
+    }
+
+    # Pass 3: recursive directory sweep (skip protected top-level roots)
+    $searchRoots = @(
+        Get-ChildItem -Path $RepoRoot -Directory -Force -ErrorAction SilentlyContinue |
+            Where-Object { -not $ProtectedTopLevel.Contains($_.Name) }
+    )
+    foreach ($dirName in $RecursiveDirNames) {
+        foreach ($root in $searchRoots) {
+            Get-ChildItem -Path $root.FullName -Filter $dirName -Recurse -Directory -Force -ErrorAction SilentlyContinue |
+                ForEach-Object { Add-Candidate -FullPath $_.FullName -Label 'recursive-dir' }
+        }
+        # searchRoots only recurses *inside* top-level dirs, so a matching dir
+        # sitting directly at repo root (e.g., $RepoRoot\__pycache__) would be
+        # missed; catch it here as a safety net.
+        Add-Candidate -FullPath (Join-Path $RepoRoot $dirName) -Label 'recursive-dir'
+    }
+
+    # Pass 4: recursive file sweep (skip protected top-level roots)
+    foreach ($pattern in $RecursiveFilePatterns) {
+        foreach ($root in $searchRoots) {
+            Get-ChildItem -Path $root.FullName -Filter $pattern -Recurse -File -Force -ErrorAction SilentlyContinue |
+                ForEach-Object { Add-Candidate -FullPath $_.FullName -Label 'recursive-file' }
+        }
+        Get-ChildItem -Path $RepoRoot -Filter $pattern -File -Force -ErrorAction SilentlyContinue |
+            ForEach-Object { Add-Candidate -FullPath $_.FullName -Label 'recursive-file' }
+    }
+
+    # Sort deepest paths first so children are removed before parents.
+    return @($candidates | Sort-Object @{ Expression = { ($_.RelativePath -split '\\').Count }; Descending = $true }, RelativePath)
+}
+
+# ── Removal ───────────────────────────────────────────────────────────────────
+
+function Remove-Artifact {
+    param([pscustomobject]$Item)
+
+    if (-not (Test-Path -LiteralPath $Item.FullPath)) {
+        return [pscustomobject]@{ Path = $Item.RelativePath; Status = 'already-absent'; Note = '' }
+    }
+
+    try {
+        Remove-Item -LiteralPath $Item.FullPath -Recurse -Force -ErrorAction Stop
+        return [pscustomobject]@{ Path = $Item.RelativePath; Status = 'removed'; Note = '' }
+    }
+    catch {
+        if (-not $RepairAcl) {
+            return [pscustomobject]@{ Path = $Item.RelativePath; Status = 'failed'; Note = $_.Exception.Message }
+        }
+        if (-not (Test-Administrator)) {
+            return [pscustomobject]@{ Path = $Item.RelativePath; Status = 'failed'; Note = 'ACL repair requires an elevated session.' }
+        }
+        try {
+            $null = takeown /F $Item.FullPath /R /D Y 2>&1
+            $null = icacls  $Item.FullPath /reset /T   2>&1
+            Remove-Item -LiteralPath $Item.FullPath -Recurse -Force -ErrorAction Stop
+            return [pscustomobject]@{ Path = $Item.RelativePath; Status = 'removed'; Note = 'ACL repaired' }
+        }
+        catch {
+            return [pscustomobject]@{ Path = $Item.RelativePath; Status = 'failed'; Note = $_.Exception.Message }
+        }
+    }
+}
+
+# ── Main ──────────────────────────────────────────────────────────────────────
+
+$candidates = Get-ArtifactCandidates -RepoRoot $repoRoot -ExcludeList $Exclude
+
+if ($candidates.Count -eq 0) {
+    Write-Host "No artifact candidates found under $repoRoot."
+    exit 0
+}
+
+Write-Host "Artifact candidates under ${repoRoot}:"
+$candidates |
+    Select-Object Label,
+                  @{ Name = 'Kind'; Expression = { if ($_.IsDirectory) { 'dir' } else { 'file' } } },
+                  RelativePath |
+    Format-Table -AutoSize |
+    Out-String |
+    Write-Host
+
+if ($ListOnly) {
+    exit 0
+}
+
+# ── Elevation for ACL repair ──────────────────────────────────────────────────
+
+if ($RepairAcl -and -not (Test-Administrator) -and -not $RelaunchedElevated) {
+    $relaunchArgs = Get-RelaunchArgumentList
+    Write-Host "Relaunching with elevation for ACL repair under $repoRoot..."
+    try {
+        $process = Start-Process -FilePath "powershell.exe" -Verb RunAs -WorkingDirectory $repoRoot -ArgumentList $relaunchArgs -Wait -PassThru
+    }
+    catch {
+        Write-Warning "Elevation was not completed. Cleanup was not performed."
+        exit 2
+    }
+    exit $process.ExitCode
+}
+
+# ── Removal ───────────────────────────────────────────────────────────────────
+
+$results = foreach ($c in $candidates) { Remove-Artifact -Item $c }
+
+$results | Format-Table Path, Status, Note -AutoSize | Out-String | Write-Host
+
+$failed = @($results | Where-Object { $_.Status -eq 'failed' })
+if ($failed.Count -gt 0) {
+    Write-Warning "$($failed.Count) item(s) could not be removed. Run with -RepairAcl to attempt ACL repair."
+    if ($RepairAcl) {
+        exit 2
+    }
+    exit 1
+}
+
+Write-Host "Repo artifact cleanup complete."
+exit 0
\ No newline at end of file
diff --git a/tests/unit/test_repo_hygiene.py b/tests/unit/test_repo_hygiene.py
index b9523c4..a827aaa 100644
--- a/tests/unit/test_repo_hygiene.py
+++ b/tests/unit/test_repo_hygiene.py
@@ -3,22 +3,17 @@
 from pathlib import Path
 
 
-def test_pytest_artifact_cleanup_script_targets_acl_poisoned_folders() -> None:
-    script = Path("scripts/cleanup_pytest_artifacts.ps1").read_text(encoding="utf-8")
+def test_repo_artifact_cleanup_script_targets_acl_poisoned_folders() -> None:
+    script = Path("scripts/cleanup_repo_artifacts.ps1").read_text(encoding="utf-8")
 
-    assert "takeown.exe" in script
-    assert "icacls.exe" in script
-    assert "pytest-cache-files-*" in script
+    assert "takeown" in script
+    assert "icacls" in script
     assert ".pytest_cache" in script
-    assert "Test-Administrator" in script
+    assert "cov_annotate" in script
     assert "RepairAcl" in script
-    assert "Start-Process" in script
-    assert "RunAs" in script
-    assert "Elevation returned, but pytest artifact targets still remain." in script
-    assert '-WorkingDirectory $repoRoot' in script
-    assert '"-NoProfile"' in script
-    assert 'Get-AllTargets -RepoRoot $repoRoot' in script
-    assert 'No pytest artifact directories were found under $repoRoot.' in script
+    assert "Get-ArtifactCandidates" in script
+    assert "Remove-Artifact" in script
+    assert "Remove-Item" in script
 
 
 def test_install_and_uninstall_scripts_support_interpreter_overrides() -> None:
@@ -39,14 +34,14 @@ def test_install_and_uninstall_scripts_support_interpreter_overrides() -> None:
     assert "Stop-Process -Id $process.ProcessId -Force" in uninstall
 
 
-def test_readme_documents_pytest_hygiene_workflow() -> None:
+def test_readme_documents_cleanup_workflow() -> None:
     readme = Path("README.md").read_text(encoding="utf-8")
 
-    assert "cleanup_pytest_artifacts.ps1" in readme
+    assert "cleanup_repo_artifacts.ps1" in readme
     assert "pytest-cache-files-*" in readme
     assert "pytest cache provider is disabled" in readme.lower()
     assert "-RepairAcl" in readme
-    assert "legacy leftovers" in readme
+    assert "cov_annotate" in readme
 
 
 def test_pytest_config_keeps_temp_output_out_of_repo() -> None: