fix(coding-agent): drain follow-ups queued during agent_end

When an extension queues a follow-up during `agent_end` it
gets stuck on the follow-up queue until after the next user
message.

Add a hasQueuedMessages() check to _handlePostAgentRun
so the existing while/continue loop drains them.

- One-line fix in _handlePostAgentRun
- Integration test in agent-session-queue
- git-merge-and-resolve example extension with tests

packages/coding-agent/examples/extensions/git-merge-and-resolve.ts

@@ -0,0 +1,115 @@
+/**
+ * Merge and Resolve
+ *
+ * Keeps the working branch up to date with its upstream tracking ref.
+ * After each agent turn, fetches and merges. Clean merges complete
+ * silently. When conflicts arise, the working tree is left dirty and
+ * the agent receives a follow-up message listing each conflict block
+ * with file, line range, and ours/theirs sections so it can resolve them.
+ * Also re-sends unresolved conflicts from a previous incomplete merge.
+ *
+ * Start pi with this extension:
+ *   pi -e ./examples/extensions/git-merge-and-resolve.ts
+ */
+import { createReadStream } from "node:fs";
+import { join } from "node:path";
+import { createInterface } from "node:readline";
+import type { ExtensionAPI } from "@earendil-works/pi-coding-agent";
+
+interface ConflictBlock {
+	file: string;
+	startLine: number;
+	separatorLine: number;
+	endLine: number;
+}
+
+/** Parse conflict markers from working tree files with unmerged paths. */
+async function findConflicts(pi: ExtensionAPI, cwd: string): Promise<ConflictBlock[]> {
+	const { stdout, code } = await pi.exec("git", ["diff", "--name-only", "--diff-filter=U"]);
+	if (code !== 0 || !stdout.trim()) return [];
+
+	const blocks: ConflictBlock[] = [];
+	for (const file of stdout.trim().split("\n")) {
+		try {
+			const rl = createInterface({ input: createReadStream(join(cwd, file), "utf-8") });
+			let lineNo = 0;
+			let blockStart: number | undefined;
+			let separatorLine: number | undefined;
+			for await (const line of rl) {
+				lineNo++;
+				if (line.startsWith("<<<<<<<")) {
+					blockStart = lineNo;
+					separatorLine = undefined;
+				} else if (line.startsWith("=======") && blockStart !== undefined) {
+					separatorLine = lineNo;
+				} else if (line.startsWith(">>>>>>>") && blockStart !== undefined && separatorLine !== undefined) {
+					blocks.push({ file, startLine: blockStart, separatorLine, endLine: lineNo });
+					blockStart = undefined;
+					separatorLine = undefined;
+				}
+			}
+		} catch {}
+	}
+	return blocks;
+}
+
+function formatRange(start: number, end: number): string {
+	if (start > end) return "empty";
+	if (start === end) return `${start}`;
+	return `${start}-${end}`;
+}
+
+function formatConflicts(ref: string, blocks: ConflictBlock[]): string {
+	const lines = [`Merged ${ref} with conflicts:`, ""];
+	for (const b of blocks) {
+		const ours = formatRange(b.startLine + 1, b.separatorLine - 1);
+		const theirs = formatRange(b.separatorLine + 1, b.endLine - 1);
+		lines.push(`  ${b.file}:${b.startLine}-${b.endLine} (ours ${ours}, theirs ${theirs})`);
+	}
+	lines.push("", "Resolve these conflicts.");
+	return lines.join("\n");
+}
+
+export default function (pi: ExtensionAPI) {
+	pi.on("agent_end", async (_event, ctx) => {
+		const { code: revParseCode } = await pi.exec("git", ["rev-parse", "--git-dir"]);
+		if (revParseCode !== 0) return;
+
+		let ref = "MERGE_HEAD";
+
+		// If not already in a merge, attempt one
+		const { code: mergeHeadCode } = await pi.exec("git", ["rev-parse", "MERGE_HEAD"]);
+		if (mergeHeadCode !== 0) {
+			// Only attempt a new merge if the working tree is clean
+			const { stdout: status } = await pi.exec("git", ["status", "--porcelain"]);
+			if (status.trim()) return;
+
+			const { stdout: upstream, code: upstreamCode } = await pi.exec("git", [
+				"rev-parse",
+				"--abbrev-ref",
+				"--symbolic-full-name",
+				"@{u}",
+			]);
+			if (upstreamCode !== 0) return;
+
+			ref = upstream.trim();
+			const remote = ref.split("/")[0];
+			ctx.ui.notify(`git-merge-and-resolve: fetching ${remote}, merging ${ref}`, "info");
+
+			const { code: fetchCode, stderr: fetchErr } = await pi.exec("git", ["fetch", remote]);
+			if (fetchCode !== 0) {
+				ctx.ui.notify(`git-merge-and-resolve: fetch failed: ${fetchErr.trim()}`, "warning");
+				return;
+			}
+
+			const { code: mergeCode } = await pi.exec("git", ["merge", "--no-ff", ref]);
+			if (mergeCode === 0) return;
+		}
+
+		// Either we just merged with conflicts, or we were already in an unfinished merge
+		const conflicts = await findConflicts(pi, ctx.cwd);
+		if (conflicts.length === 0) return;
+
+		pi.sendUserMessage(formatConflicts(ref, conflicts), { deliverAs: "followUp" });
+	});
+}