fix(memory): extractTranscriptFromActivity now reads custom_message entries

Activity JSONL logs use `type: "custom_message"` with `customType: "sf-auto"`
for assistant reasoning content. The old code only checked `role === "assistant"`,
so every transcript was empty → extraction silently skipped every unit.

Fix: recognise both legacy (`role === "assistant"`) and modern
(`custom_message` with `sf-*` prefix) entry shapes. Also reads the
standalone `text` field used by custom messages.

This is why memory_processed_units had 0 rows despite 34 activity logs.

Tests: 186 files / 1994 tests pass.
Type check: clean.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/resources/extensions/sf/memory-extractor.js

@@ -153,32 +153,39 @@ function extractTranscriptFromActivity(raw, maxChars = 30_000) {
 	const lines = raw.split("\n");
 	const parts = [];
 	let totalChars = 0;
+	function appendText(text) {
+		if (totalChars + text.length > maxChars) {
+			parts.push(text.substring(0, maxChars - totalChars));
+			return false; // signal stop
+		}
+		parts.push(text);
+		totalChars += text.length;
+		return true;
+	}
 	for (const line of lines) {
 		if (!line.trim()) continue;
 		try {
 			const entry = JSON.parse(line);
-			if (entry.role !== "assistant") continue;
+			// Modern activity logs use custom_message with customType "sf-auto"
+			// for assistant reasoning; legacy logs use role === "assistant".
+			const isAssistant =
+				entry.role === "assistant" ||
+				(entry.type === "custom_message" &&
+					entry.customType?.startsWith("sf-"));
+			if (!isAssistant) continue;
 			// Handle content array or direct text
 			if (Array.isArray(entry.content)) {
 				for (const block of entry.content) {
 					if (block.type === "text" && block.text) {
-						const text = block.text;
-						if (totalChars + text.length > maxChars) {
-							parts.push(text.substring(0, maxChars - totalChars));
-							return parts.join("\n\n");
-						}
-						parts.push(text);
-						totalChars += text.length;
+						if (!appendText(block.text)) return parts.join("\n\n");
 					}
 				}
-			} else if (typeof entry.content === "string") {
-				const text = entry.content;
-				if (totalChars + text.length > maxChars) {
-					parts.push(text.substring(0, maxChars - totalChars));
-					return parts.join("\n\n");
-				}
-				parts.push(text);
-				totalChars += text.length;
+			} else if (typeof entry.content === "string" && entry.content) {
+				if (!appendText(entry.content)) return parts.join("\n\n");
+			}
+			// Also read plain text/content field on custom_message entries
+			if (entry.text && typeof entry.text === "string") {
+				if (!appendText(entry.text)) return parts.join("\n\n");
 			}
 		} catch {
 			// Skip malformed lines

src/tests/headless-mark-state.test.ts

@@ -0,0 +1,79 @@
+/**
+ * Smoke test for the headless complete-slice / skip-slice /
+ * complete-milestone commands (#mark-state).
+ *
+ * The full handler is exercised against a real SF project DB by
+ * dogfooding it on dr-repo's stale M003/S01 placeholder — see the
+ * commit message for the live run. Here we just check the dispatch
+ * surface and the help text so regressions are caught fast.
+ */
+
+import assert from "node:assert/strict";
+import { readFileSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { fileURLToPath } from "node:url";
+import { test } from "vitest";
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const headlessSrc = readFileSync(join(__dirname, "..", "headless.ts"), "utf-8");
+const helpSrc = readFileSync(join(__dirname, "..", "help-text.ts"), "utf-8");
+const handlerSrc = readFileSync(
+	join(__dirname, "..", "headless-mark-state.ts"),
+	"utf-8",
+);
+
+test("headless.ts dispatches the three new commands to handleMarkState", () => {
+	assert.match(
+		headlessSrc,
+		/options\.command === "complete-slice"/,
+		"complete-slice must be dispatched",
+	);
+	assert.match(
+		headlessSrc,
+		/options\.command === "skip-slice"/,
+		"skip-slice must be dispatched",
+	);
+	assert.match(
+		headlessSrc,
+		/options\.command === "complete-milestone"/,
+		"complete-milestone must be dispatched",
+	);
+	assert.match(
+		headlessSrc,
+		/import\("\.\/headless-mark-state\.js"\)/,
+		"headless.ts must import the new handler",
+	);
+});
+
+test("help text lists the three new commands", () => {
+	assert.match(helpSrc, /complete-slice\s+Mark a slice complete/);
+	assert.match(helpSrc, /skip-slice\s+Mark a slice skipped/);
+	assert.match(helpSrc, /complete-milestone\s+Mark a milestone complete/);
+});
+
+test("handler refuses missing positional and bad ref shapes", () => {
+	// Spot-checks the documented error paths so a refactor doesn't drop them.
+	assert.match(
+		handlerSrc,
+		/requires a reference \(e\.g\. M010\/S03\)/,
+		"missing-ref error must remain user-readable",
+	);
+	assert.match(
+		handlerSrc,
+		/complete-milestone takes a milestone id, not <M>\/<S>/,
+		"milestone-ref shape error must remain user-readable",
+	);
+	assert.match(
+		handlerSrc,
+		/requires <milestone>\/<slice> \(e\.g\. M010\/S03\)/,
+		"slice-ref shape error must remain user-readable",
+	);
+});
+
+test("handler is idempotent on already-closed targets", () => {
+	// The handler short-circuits with {ok: true, idempotent: true}
+	// rather than failing — important for scripting.
+	assert.match(handlerSrc, /idempotent: true/);
+	assert.match(handlerSrc, /already \$\{targetStatus\}/);
+	assert.match(handlerSrc, /already complete/);
+});