refactor,docs,ci: complete compat cleanup and layout config separation

This commit finalizes several key architectural and cleanup tasks:
1.  Restructures document layout policy out of the hardcoded artifact shell into a standalone configurable system
2.  Extracts legacy compatibility helpers into a dedicated module
3.  Updates all documentation to reflect the new layered architecture
4.  Adds proper diagnostic severity tracking and warning handling
5.  Splits render config resolution into explicit resolve + parse API
6.  Adds full compat cleanup todo list and completes initial documentation overhauls
7.  Fixes markdownlint coverage and test assertions
8.  Updates CI/verify scripts to properly filter error diagnostics

Author: Sayhi-bzb

.markdownlint-cli2.jsonc

@@ -7,6 +7,7 @@
   "globs": [
     "README.md",
     "blueprint/**/*.md",
+    "docs/**/*.md",
     "spec/**/*.md",
     "!node_modules",
     "!dist",

apps/agent-html-app/src/app.tsx

@@ -1560,9 +1560,11 @@ export function App() {
             >
               {commandState.runningDoctor ? "Checking..." : "Doctor"}
             </Button>
-            <StatusBadge>{isTauriRuntime() ? "Tauri" : "Mock"}</StatusBadge>
+            <span className="shell-inline-status">
+              {isTauriRuntime() ? "Tauri" : "Mock"}
+            </span>
             {commandState.error ? (
-              <StatusBadge tone="error">Error</StatusBadge>
+              <span className="shell-inline-status status-error">Error</span>
             ) : null}
           </div>
         </div>
@@ -1589,13 +1591,14 @@ export function App() {
         <SurfaceCardBody className="stage-banner-body" padding="compact">
           <div className="stage-banner-copy">
             <div className="stage-banner-headline">
+              <span className="eyebrow stage-eyebrow">Flow</span>
               <strong>{currentStageItem?.label ?? "Current stage"}</strong>
               <div className="stage-banner-meta">
-                <StatusBadge
-                  tone={statusToneForStage(currentStageItem?.pillClassName)}
+                <span
+                  className={`shell-inline-status ${currentStageItem?.pillClassName ?? ""}`}
                 >
                   {currentStageItem?.statusLabel ?? "Current"}
-                </StatusBadge>
+                </span>
                 <span className="inline-meta">View {activeView}</span>
               </div>
             </div>
@@ -1614,16 +1617,6 @@ export function App() {
                 {currentStageAction.label}
               </Button>
             ) : null}
-            <Button
-              onClick={() => {
-                void copyText(appState.currentSession.sourcePath)
-              }}
-              size="sm"
-              type="button"
-              variant="outline"
-            >
-              Copy source path
-            </Button>
           </div>
         </SurfaceCardBody>
       </SurfaceCard>