chore: add marker removal detection to CI and regression guard tests

Two new safety nets prevent `altimate_change` markers from being silently removed:

1. **CI marker guard** (`analyze.ts --markers`): now detects net marker removal
   in diffs — if more markers are deleted than added, the check warns/fails.
   This is what would have caught #316 before merge.

2. **Regression test** (`upstream-merge-guard.test.ts`): minimum marker count
   per file. If a file's marker count drops below its recorded floor, the test
   fails. Counts must be updated when adding new markers (never lowered).

Also adds `tool/bash.ts`, `tool/skill.ts`, and `skill/skill.ts` to the
`requiredMarkerFiles` list so their marker presence is enforced.

Closes #321

Author: anandgupta42

packages/opencode/test/branding/upstream-merge-guard.test.ts

@@ -483,6 +483,9 @@ describe("altimate_change marker integrity", () => {
     "src/index.ts",
     "src/agent/agent.ts",
     "src/tool/registry.ts",
+    "src/tool/bash.ts",
+    "src/tool/skill.ts",
+    "src/skill/skill.ts",
     "src/telemetry/index.ts",
     "src/global/index.ts",
     "src/util/token.ts",
@@ -514,4 +517,36 @@ describe("altimate_change marker integrity", () => {
 
     expect(mismatched).toEqual([])
   })
+
+  // Minimum marker counts per file — prevents accidental marker removal.
+  // When you ADD markers to a file, update the count here. If a count drops,
+  // it means someone removed markers that protected custom code from upstream overwrites.
+  const minimumMarkerCounts: Record<string, number> = {
+    "src/session/compaction.ts": 2,
+    "src/session/prompt.ts": 2,
+    "src/installation/index.ts": 2,
+    "src/flag/flag.ts": 2,
+    "src/config/config.ts": 2,
+    "src/config/paths.ts": 2,
+    "src/index.ts": 2,
+    "src/agent/agent.ts": 2,
+    "src/tool/registry.ts": 2,
+    "src/tool/bash.ts": 2,
+    "src/tool/skill.ts": 20,
+    "src/skill/skill.ts": 8,
+    "src/telemetry/index.ts": 2,
+    "src/global/index.ts": 2,
+    "src/util/token.ts": 2,
+    "src/storage/db.ts": 2,
+  }
+
+  for (const [relPath, minCount] of Object.entries(minimumMarkerCounts)) {
+    test(`${relPath} has at least ${minCount} altimate_change markers (regression guard)`, () => {
+      const fullPath = join(pkgDir, relPath)
+      expect(existsSync(fullPath)).toBe(true)
+      const content = readText(fullPath)
+      const actual = (content.match(/altimate_change/g) || []).length
+      expect(actual).toBeGreaterThanOrEqual(minCount)
+    })
+  }
 })

script/upstream/analyze.ts

@@ -631,20 +631,27 @@ function checkFileForMarkers(file: string, base?: string): MarkerWarning[] {
   let newCodeStart = 0
   let newCodeContext = ""
 
+  // Track marker additions and removals to detect net marker loss.
+  // A removed marker line (prefixed with -) without a corresponding addition
+  // means someone deleted a marker while keeping or modifying the code it protected.
+  let markersAdded = 0
+  let markersRemoved = 0
+  let firstRemovedMarkerContext = ""
+
   for (const line of lines) {
-    const hunkMatch = line.match(/^@@ -\d+(?:,\d+)? \+(\d+)/)
+    const hunkMatch = line.match(/^@@ -(\d+)(?:,\d+)? \+(\d+)/)
     if (hunkMatch) {
-      currentLine = parseInt(hunkMatch[1]) - 1
+      currentLine = parseInt(hunkMatch[2]) - 1
       continue
     }
 
     if (line.startsWith("+") && !line.startsWith("+++")) {
       currentLine++
       const content = line.slice(1).trim()
 
-      if (content.includes("altimate_change start")) { inMarkerBlock = true; continue }
-      if (content.includes("altimate_change end")) { inMarkerBlock = false; continue }
-      if (content.includes("altimate_change")) continue
+      if (content.includes("altimate_change start")) { inMarkerBlock = true; markersAdded++; continue }
+      if (content.includes("altimate_change end")) { inMarkerBlock = false; markersAdded++; continue }
+      if (content.includes("altimate_change")) { markersAdded++; continue }
 
       if (!content) continue
       if (content.startsWith("//") && !content.includes("TODO")) continue
@@ -658,8 +665,15 @@ function checkFileForMarkers(file: string, base?: string): MarkerWarning[] {
           newCodeContext = content
         }
       }
-    } else if (line.startsWith("-")) {
-      // deleted line, don't increment
+    } else if (line.startsWith("-") && !line.startsWith("---")) {
+      // deleted line, don't increment currentLine
+      const content = line.slice(1).trim()
+      if (content.includes("altimate_change")) {
+        markersRemoved++
+        if (!firstRemovedMarkerContext) {
+          firstRemovedMarkerContext = content.slice(0, 80)
+        }
+      }
     } else {
       currentLine++
     }
@@ -674,6 +688,17 @@ function checkFileForMarkers(file: string, base?: string): MarkerWarning[] {
     })
   }
 
+  // Detect net marker removal: more markers deleted than added means protection was stripped.
+  if (markersRemoved > markersAdded) {
+    const net = markersRemoved - markersAdded
+    warnings.push({
+      file,
+      line: 0,
+      context: firstRemovedMarkerContext,
+      reason: `${net} altimate_change marker(s) removed — custom code may lose upstream merge protection`,
+    })
+  }
+
   return warnings
 }