docs: document intentional design decisions in atlas, todo-continuation, and delegation hooks

src/hooks/atlas/sisyphus-path.ts

@@ -1,6 +1,7 @@
 /**
  * Cross-platform check if a path is inside .sisyphus/ directory.
  * Handles both forward slashes (Unix) and backslashes (Windows).
+ * Uses path segment matching (not substring) to avoid false positives like "not-sisyphus/file.txt"
  */
 export function isSisyphusPath(filePath: string): boolean {
   return /\.sisyphus[/\\]/.test(filePath)

src/hooks/atlas/tool-execute-before.ts

@@ -20,6 +20,7 @@ export function createToolExecuteBeforeHandler(input: {
     }
 
     // Check Write/Edit tools for orchestrator - inject strong warning
+    // Warn-only policy: Atlas guides orchestrators toward delegation but doesn't block, allowing flexibility for urgent fixes
     if (isWriteOrEditToolName(toolInput.tool)) {
       const filePath = (toolOutput.args.filePath ?? toolOutput.args.path ?? toolOutput.args.file) as string | undefined
       if (filePath && !isSisyphusPath(filePath)) {