From 2b830c889928d3fda8c5563d0684c5745e1fa0f0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 27 Apr 2026 18:16:48 +0000
Subject: [PATCH 1/2] Initial plan


From 3f3709f40bcb667c01c52b43fb43cb27d84c86f3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 27 Apr 2026 18:21:30 +0000
Subject: [PATCH 2/2] fix: remove stale .bot/recipes and .bot/workflow.yaml
 from ProtectedPaths; skip non-existent paths in git add during init --force

Agent-Logs-Url: https://github.com/andresharpe/dotbot/sessions/501a7a91-56dd-4eb3-bbaa-502ffcfbe41e

Co-authored-by: andresharpe <7415999+andresharpe@users.noreply.github.com>
---
 core/mcp/modules/FrameworkIntegrity.psm1 | 2 --
 scripts/init-project.ps1                 | 9 ++++++++-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/core/mcp/modules/FrameworkIntegrity.psm1 b/core/mcp/modules/FrameworkIntegrity.psm1
index 0ee93475..0144f60c 100644
--- a/core/mcp/modules/FrameworkIntegrity.psm1
+++ b/core/mcp/modules/FrameworkIntegrity.psm1
@@ -23,13 +23,11 @@
 $script:ProtectedPaths = @(
     '.bot/core',
     '.bot/hooks',
-    '.bot/recipes',
     '.bot/settings/providers',
     '.bot/settings/settings.default.json',
     '.bot/settings/theme.default.json',
     '.bot/go.ps1',
     '.bot/init.ps1',
-    '.bot/workflow.yaml',
     '.bot/.gitignore',
     '.bot/.manifest.json',
     '.bot/README.md'
diff --git a/scripts/init-project.ps1 b/scripts/init-project.ps1
index f9f8e2cc..c176b4fc 100644
--- a/scripts/init-project.ps1
+++ b/scripts/init-project.ps1
@@ -1267,7 +1267,14 @@ if ($LASTEXITCODE -ne 0) {
     $dirty = git -C $ProjectDir status --porcelain -- @stagePaths 2>$null
     if ($dirty) {
         Write-DotbotCommand "Committing framework file updates..."
-        git -C $ProjectDir add -- @stagePaths 2>$null
+        # Filter to paths that actually exist so git add never aborts on a
+        # missing pathspec (e.g. retired paths still listed in an old manifest).
+        $existingStagePaths = $stagePaths | Where-Object {
+            Test-Path -LiteralPath (Join-Path $ProjectDir $_)
+        }
+        if ($existingStagePaths) {
+            git -C $ProjectDir add -- @existingStagePaths
+        }
         $rc = Submit-ForceCommit -Root $ProjectDir -Message "chore: update dotbot framework files"
         if ($rc -eq 0) {
             Write-Success "Framework update committed"