refactor: reorganize client transport and extension internals

- Split client, native, remote, serve, markdown, and SDK internals into focused packages with direct imports.
- Move local and remote transport framing/protocol helpers behind clearer module boundaries.
- Break up the extension injected DOM logic into a separate content dispatch bundle and dedicated content modules.
- Add explicit client handling for passive remote discovery without noisy PQ warnings.
- Keep behavior covered with updated unit, integration, and extension tests.

extension/src/commands/tabs.ts

@@ -23,12 +23,15 @@ export class TabsMutationCommands extends CommandGroup {
     return runLargeOperation("tabs.close", async () => {
       let toClose: number[] = [];
       if (duplicates) {
-        const all = await chrome.tabs.query({});
-        const seen = new Set();
-        for (const t of all) {
-          if (!t.url) continue;
-          if (seen.has(t.url)) toClose.push(t.id);
-          else seen.add(t.url);
+        const windows = await chrome.windows.getAll({ populate: true });
+        const seen = new Set<string>();
+        for (const w of windows) {
+          for (const t of w.tabs || []) {
+            const url = t.url || t.pendingUrl;
+            if (!url || t.id == null) continue;
+            if (seen.has(url)) toClose.push(t.id);
+            else seen.add(url);
+          }
         }
       } else if (inactive) {
         const all = await chrome.tabs.query({});