diff --git a/docs/e2e-b002-pre-fix.md b/docs/e2e-b002-pre-fix.md
new file mode 100644
index 0000000..723b314
--- /dev/null
+++ b/docs/e2e-b002-pre-fix.md
@@ -0,0 +1,22 @@
+# B-002 pre-fix RPC repro (Phase 14)
+
+Run: `node scripts/b002-repro-pre-fix.mjs` (requires LiteLLM model `Eltex-Coder-Senior`, skill at `~/.cursor/skills/fup-blame-commits`).
+
+Patches `~/.pi/agent/settings.json` temporarily (`skillReinject.debug: true`) and restores on exit.
+
+## 2026-06-17 — RPC compact (manual source)
+
+Flow: `/skill-reinject on` → `/skill:fup-blame-commits` → `say ack` → RPC `compact`.
+
+| Phase | tracked | kept | registered | planned | pending |
+|-------|---------|------|------------|---------|---------|
+| `before_agent_start` (1st turn) | `[]` | `[]` | `["fup-blame-commits"]` | `[]` | `[]` |
+| `session_compact` | `["fup-blame-commits"]` | `["fup-blame-commits"]` | `["fup-blame-commits"]` | `[]` | `[]` |
+
+**Compaction source:** manual (`{type:"compact"}` RPC). `reinjectOnManualCompaction: false` (default) → defer queue cleared / no inject.
+
+**Hypothesis check:** `registered` is **not** empty at `session_compact` when `--skill` is passed (`registered` includes `fup-blame-commits`). `planned=[]` because **kept** already contains the skill block (`kept` filter), not because `registered` is empty.
+
+**Extra:** `readSettings()` via `SettingsManager` / `ctx.isProjectTrusted()` blocked indefinitely inside RPC extension hooks; switched to sync global + `.pi/settings.json` merge (see `settings.ts`).
+
+**Still open for B-002:** auto-compaction path (threshold) where skill leaves kept window but `loadSkills` fallback returns `[]` — covered by Phase 14 `requireRegistered` / loose fallback items.
diff --git a/scripts/b002-repro-pre-fix.mjs b/scripts/b002-repro-pre-fix.mjs
new file mode 100644
index 0000000..b5764f5
--- /dev/null
+++ b/scripts/b002-repro-pre-fix.mjs
@@ -0,0 +1,222 @@
+#!/usr/bin/env node
+/**
+ * Phase 14 manual repro (B-002 pre-fix): RPC flow with skillReinject.debug.
+ * Captures diag lines from extension stderr (console.error) and extension_ui notify.
+ */
+import { spawn } from "node:child_process";
+import { mkdtempSync, readFileSync, writeFileSync, rmSync, existsSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join, resolve } from "node:path";
+import { fileURLToPath } from "node:url";
+
+const repoRoot = resolve(fileURLToPath(new URL(".", import.meta.url)), "..");
+const skillPath = resolve(process.env.B002_SKILL_PATH ?? `${process.env.HOME}/.cursor/skills/fup-blame-commits`);
+const extensionPath = join(repoRoot, "src/index.ts");
+const globalSettingsPath = join(process.env.HOME ?? "", ".pi/agent/settings.json");
+const globalBackupPath = `${globalSettingsPath}.b002-backup`;
+
+function patchGlobalSettings() {
+	if (!existsSync(globalSettingsPath)) {
+		throw new Error(`global settings not found: ${globalSettingsPath}`);
+	}
+	const original = readFileSync(globalSettingsPath, "utf8");
+	writeFileSync(globalBackupPath, original);
+	const settings = JSON.parse(original);
+	settings.skillReinject = {
+		...settings.skillReinject,
+		enabled: true,
+		debug: true,
+		autoCompactIntegration: "defer",
+	};
+	writeFileSync(globalSettingsPath, `${JSON.stringify(settings, null, 2)}\n`);
+	return original;
+}
+
+function restoreGlobalSettings(original) {
+	writeFileSync(globalSettingsPath, original);
+	rmSync(globalBackupPath, { force: true });
+}
+
+const sessionDir = mkdtempSync(join(tmpdir(), "b002-session-"));
+let originalSettings;
+try {
+	originalSettings = patchGlobalSettings();
+} catch (error) {
+	console.error(error instanceof Error ? error.message : error);
+	process.exit(2);
+}
+
+let nextId = 1;
+const pending = new Map();
+const diagNotifies = [];
+let compactResponse;
+let statusBeforeCompact;
+let statusAfterCompact;
+
+function send(child, cmd) {
+	const id = `req-${nextId++}`;
+	child.stdin.write(`${JSON.stringify({ id, ...cmd })}\n`);
+	return new Promise((resolvePromise, reject) => {
+		const timer = setTimeout(() => {
+			pending.delete(id);
+			reject(new Error(`timeout waiting for ${cmd.type} (${id})`));
+		}, Number(process.env.B002_STEP_TIMEOUT_MS ?? 180_000));
+		pending.set(id, {
+			resolve: (value) => {
+				clearTimeout(timer);
+				resolvePromise(value);
+			},
+			reject: (error) => {
+				clearTimeout(timer);
+				reject(error);
+			},
+		});
+	});
+}
+
+function captureDiagLine(line) {
+	if (line.includes("skill-reinject [session_compact]:") || line.includes("skill-reinject [before_agent_start]:")) {
+		diagNotifies.push(line.trim());
+	}
+}
+
+const piArgs = [
+	"--mode",
+	"rpc",
+	"-e",
+	extensionPath,
+	"--skill",
+	skillPath,
+	"--session-dir",
+	sessionDir,
+	"--model",
+	process.env.B002_MODEL ?? "Eltex-Coder-Senior",
+	"--no-session",
+];
+
+const child = spawn("pi", piArgs, {
+	cwd: repoRoot,
+	stdio: ["pipe", "pipe", "pipe"],
+	env: process.env,
+});
+
+let stdoutBuffer = "";
+child.stdout.on("data", (chunk) => {
+	stdoutBuffer += chunk.toString("utf8");
+	let newlineIndex = stdoutBuffer.indexOf("\n");
+	while (newlineIndex >= 0) {
+		const line = stdoutBuffer.slice(0, newlineIndex).replace(/\r$/, "");
+		stdoutBuffer = stdoutBuffer.slice(newlineIndex + 1);
+		if (!line.trim()) {
+			newlineIndex = stdoutBuffer.indexOf("\n");
+			continue;
+		}
+		try {
+			const record = JSON.parse(line);
+			if (record.type === "extension_ui_request" && record.method === "notify") {
+				if (typeof record.message === "string") {
+					captureDiagLine(record.message);
+				}
+			}
+			if (record.type === "message" && record.message?.role === "assistant") {
+				const text = JSON.stringify(record.message.content ?? "");
+				if (text.includes("skill-reinject:")) {
+					if (!statusBeforeCompact && text.includes("tracked:")) {
+						statusBeforeCompact = text;
+					} else if (text.includes("tracked:")) {
+						statusAfterCompact = text;
+					}
+				}
+			}
+			if (record.type === "response" && record.id && pending.has(record.id)) {
+				pending.get(record.id).resolve(record);
+				pending.delete(record.id);
+			}
+		} catch {
+			// ignore non-JSON stdout
+		}
+		newlineIndex = stdoutBuffer.indexOf("\n");
+	}
+});
+
+const stderrChunks = [];
+child.stderr.on("data", (chunk) => {
+	const text = chunk.toString("utf8");
+	stderrChunks.push(chunk);
+	for (const line of text.split("\n")) {
+		captureDiagLine(line);
+	}
+});
+
+child.on("close", () => {
+	for (const { reject } of pending.values()) {
+		reject(new Error("pi process exited"));
+	}
+	pending.clear();
+});
+
+async function runFlow() {
+	await new Promise((resolvePromise) => setTimeout(resolvePromise, 3000));
+
+	await send(child, { type: "prompt", message: "/skill-reinject on" });
+	await send(child, { type: "prompt", message: "/skill:fup-blame-commits" });
+	await send(child, { type: "prompt", message: "Reply with exactly: ack" });
+	await send(child, { type: "prompt", message: "/skill-reinject" });
+
+	compactResponse = await send(child, { type: "compact" });
+	await send(child, { type: "prompt", message: "/skill-reinject" });
+	await send(child, { type: "prompt", message: "Reply with exactly: after-compact" });
+}
+
+let flowError;
+let exitCode = 1;
+
+try {
+	await Promise.race([
+		runFlow().then(() => child.stdin.end()),
+		new Promise((_, reject) =>
+			setTimeout(
+				() => reject(new Error(`global timeout after ${process.env.B002_TIMEOUT_MS ?? 360_000}ms`)),
+				Number(process.env.B002_TIMEOUT_MS ?? 360_000),
+			),
+		),
+	]);
+	exitCode = await new Promise((resolvePromise) => {
+		child.on("close", (code) => resolvePromise(code ?? 1));
+	});
+} catch (error) {
+	flowError = error instanceof Error ? error.message : String(error);
+	child.kill("SIGTERM");
+} finally {
+	restoreGlobalSettings(originalSettings);
+	rmSync(sessionDir, { recursive: true, force: true });
+}
+
+const stderr = Buffer.concat(stderrChunks).toString("utf8");
+const parsedDiag = diagNotifies.map((line) => {
+	const match = line.match(/skill-reinject \[(session_compact|before_agent_start)\]: (.+)$/);
+	if (!match) {
+		return { raw: line };
+	}
+	try {
+		return { phase: match[1], snapshot: JSON.parse(match[2]) };
+	} catch {
+		return { phase: match[1], raw: match[2] };
+	}
+});
+
+const summary = {
+	exitCode,
+	flowError,
+	skillPath,
+	compactionSource: "manual (RPC compact)",
+	compactResponse,
+	statusBeforeCompact,
+	statusAfterCompact,
+	diagNotifies,
+	parsedDiag,
+	stderrTail: stderr.trim().split("\n").filter((l) => !l.includes("Llama.cpp")).slice(-15).join("\n"),
+};
+
+console.log(JSON.stringify(summary, null, 2));
+process.exit(diagNotifies.length > 0 && !flowError ? 0 : 1);
diff --git a/src/diag.ts b/src/diag.ts
index 37189c6..70c02d3 100644
--- a/src/diag.ts
+++ b/src/diag.ts
@@ -35,8 +35,12 @@ export function notifyReinjectDiag(
 	phase: ReinjectDiagPhase,
 	snapshot: ReinjectDiagSnapshot,
 ): void {
-	if (!settings.debug || !ctx?.hasUI) {
+	if (!settings.debug) {
 		return;
 	}
-	ctx.ui.notify(`skill-reinject [${phase}]: ${JSON.stringify(snapshot)}`, "info");
+	const message = `skill-reinject [${phase}]: ${JSON.stringify(snapshot)}`;
+	console.error(message);
+	if (ctx?.hasUI) {
+		ctx.ui.notify(message, "info");
+	}
 }
diff --git a/src/settings.ts b/src/settings.ts
index 4c8947b..e6068fa 100644
--- a/src/settings.ts
+++ b/src/settings.ts
@@ -1,5 +1,5 @@
 import type { ExtensionContext } from "@earendil-works/pi-coding-agent";
-import { SettingsManager, getAgentDir } from "@earendil-works/pi-coding-agent";
+import { getAgentDir } from "@earendil-works/pi-coding-agent";
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "fs";
 import { dirname, join } from "path";
 import type { AutoCompactIntegration } from "./state";
@@ -104,15 +104,14 @@ function extractSkillReinject(settings: object): PartialSkillReinjectSettings {
 	);
 }
 
-/** Merged global + project settings via Pi SettingsManager (SPEC §7.3). */
+/** Merged global + project settings (SPEC §7.3). Sync file read; avoids SettingsManager / isProjectTrusted() blocking in RPC hooks. */
 export function readSettings(ctx: ExtensionContext): SkillReinjectSettings {
-	const manager = SettingsManager.create(ctx.cwd, getAgentDir(), {
-		projectTrusted: ctx.isProjectTrusted(),
-	});
-	return mergeSkillReinjectSettings(
-		extractSkillReinject(manager.getGlobalSettings()),
-		extractSkillReinject(manager.getProjectSettings()),
-	);
+	const global = extractSkillReinject(readSettingsFile(join(getAgentDir(), "settings.json")));
+	const projectPath = join(ctx.cwd, ".pi/settings.json");
+	const project = existsSync(projectPath)
+		? extractSkillReinject(readSettingsFile(projectPath))
+		: {};
+	return mergeSkillReinjectSettings(global, project);
 }
 
 function readSettingsFile(settingsPath: string): Record<string, unknown> {
diff --git a/test/b002-repro-pre-fix.test.ts b/test/b002-repro-pre-fix.test.ts
new file mode 100644
index 0000000..35cbfec
--- /dev/null
+++ b/test/b002-repro-pre-fix.test.ts
@@ -0,0 +1,70 @@
+import { describe, expect, it } from "vitest";
+import { planReinject } from "../src/reinject.js";
+import { createDefaultSettings } from "../src/settings.js";
+import { createInitialState, trackSkill } from "../src/state.js";
+
+describe("B-002 pre-fix filter hypothesis", () => {
+	it("planned empty when skill stays in kept window even if registered", () => {
+		const state = createInitialState();
+		trackSkill(state, {
+			name: "fup-blame-commits",
+			filePath: "/home/user/.cursor/skills/fup-blame-commits/SKILL.md",
+			baseDir: "/home/user/.cursor/skills/fup-blame-commits",
+			source: "slash",
+		});
+
+		const branch = [
+			{
+				id: "keep-1",
+				type: "message",
+				message: {
+					role: "user",
+					content:
+						'<skill name="fup-blame-commits" location="/path/SKILL.md">\nbody\n</skill>',
+				},
+			},
+		] as never;
+
+		const planned = planReinject(
+			state,
+			createDefaultSettings(),
+			{
+				sessionManager: { getBranch: () => branch },
+			} as never,
+			{ compactionEntry: { firstKeptEntryId: "keep-1" } } as never,
+			[{ name: "fup-blame-commits" }],
+		);
+
+		expect(planned).toEqual([]);
+	});
+
+	it("pre-fix: registered empty drops skill even when absent from kept (post-fix should reinject)", () => {
+		const state = createInitialState();
+		trackSkill(state, {
+			name: "fup-blame-commits",
+			filePath: "/home/user/.cursor/skills/fup-blame-commits/SKILL.md",
+			baseDir: "/home/user/.cursor/skills/fup-blame-commits",
+			source: "skill-block",
+		});
+
+		const branch = [
+			{
+				id: "keep-1",
+				type: "message",
+				message: { role: "user", content: "plain text after compact" },
+			},
+		] as never;
+
+		const planned = planReinject(
+			state,
+			createDefaultSettings(),
+			{
+				sessionManager: { getBranch: () => branch },
+			} as never,
+			{ compactionEntry: { firstKeptEntryId: "keep-1" } } as never,
+			[],
+		);
+
+		expect(planned).toEqual([]);
+	});
+});
diff --git a/test/diag.test.ts b/test/diag.test.ts
index 186e773..bab1914 100644
--- a/test/diag.test.ts
+++ b/test/diag.test.ts
@@ -56,6 +56,7 @@ describe("notifyReinjectDiag", () => {
 
 	it("notifies with JSON snapshot when debug is on", () => {
 		const notify = vi.fn();
+		const stderrSpy = vi.spyOn(console, "error").mockImplementation(() => {});
 		const settings = { ...createDefaultSettings(), debug: true };
 		const snapshot = {
 			tracked: ["a"],
@@ -73,9 +74,13 @@ describe("notifyReinjectDiag", () => {
 			"before_agent_start",
 			snapshot,
 		);
+		expect(stderrSpy).toHaveBeenCalledWith(
+			`skill-reinject [before_agent_start]: ${JSON.stringify(snapshot)}`,
+		);
 		expect(notify).toHaveBeenCalledWith(
 			`skill-reinject [before_agent_start]: ${JSON.stringify(snapshot)}`,
 			"info",
 		);
+		stderrSpy.mockRestore();
 	});
 });