@oh-my-pi/pi-coding-agent 13.15.3 → 13.16.1

package/src/modes/rpc/rpc-mode.ts

@@ -29,6 +29,77 @@ import type {
 // Re-export types for consumers
 export type * from "./rpc-types";
 
+export type PendingExtensionRequest = {
+	resolve: (response: RpcExtensionUIResponse) => void;
+	reject: (error: Error) => void;
+};
+
+type RpcOutput = (obj: RpcResponse | RpcExtensionUIRequest | object) => void;
+
+export function requestRpcEditor(
+	pendingRequests: Map<string, PendingExtensionRequest>,
+	output: RpcOutput,
+	title: string,
+	prefill?: string,
+	dialogOptions?: ExtensionUIDialogOptions,
+	editorOptions?: { promptStyle?: boolean },
+): Promise<string | undefined> {
+	if (dialogOptions?.signal?.aborted) return Promise.resolve(undefined);
+
+	const id = Snowflake.next() as string;
+	const { promise, resolve, reject } = Promise.withResolvers<string | undefined>();
+	let settled = false;
+
+	const cleanup = () => {
+		dialogOptions?.signal?.removeEventListener("abort", onAbort);
+		pendingRequests.delete(id);
+	};
+	const finish = (value: string | undefined) => {
+		if (settled) return;
+		settled = true;
+		cleanup();
+		resolve(value);
+	};
+	const fail = (error: Error) => {
+		if (settled) return;
+		settled = true;
+		cleanup();
+		reject(error);
+	};
+	const onAbort = () => {
+		output({
+			type: "extension_ui_request",
+			id: Snowflake.next() as string,
+			method: "cancel",
+			targetId: id,
+		} as RpcExtensionUIRequest);
+		finish(undefined);
+	};
+
+	dialogOptions?.signal?.addEventListener("abort", onAbort, { once: true });
+	pendingRequests.set(id, {
+		resolve: response => {
+			if ("cancelled" in response && response.cancelled) {
+				finish(undefined);
+			} else if ("value" in response) {
+				finish(response.value);
+			} else {
+				finish(undefined);
+			}
+		},
+		reject: fail,
+	});
+	output({
+		type: "extension_ui_request",
+		id,
+		method: "editor",
+		title,
+		prefill,
+		promptStyle: editorOptions?.promptStyle,
+	} as RpcExtensionUIRequest);
+	return promise;
+}
+
 /**
  * Run in RPC mode.
  * Listens for JSON commands on stdin, outputs events and responses on stdout.
@@ -55,12 +126,6 @@ export async function runRpcMode(session: AgentSession): Promise<never> {
 		return { id, type: "response", command, success: false, error: message };
 	};
 
-	// Pending extension UI requests waiting for response
-	type PendingExtensionRequest = {
-		resolve: (response: RpcExtensionUIResponse) => void;
-		reject: (error: Error) => void;
-	};
-
 	const pendingExtensionRequests = new Map<string, PendingExtensionRequest>();
 
 	// Shutdown request flag (wrapped in object to allow mutation with const)
@@ -261,30 +326,13 @@ export async function runRpcMode(session: AgentSession): Promise<never> {
 			return "";
 		}
 
-		async editor(title: string, prefill?: string): Promise<string | undefined> {
-			const id = Snowflake.next() as string;
-			const { promise, resolve, reject } = Promise.withResolvers<string | undefined>();
-			this.pendingRequests.set(id, {
-				resolve: (response: RpcExtensionUIResponse) => {
-					this.pendingRequests.delete(id);
-					if ("cancelled" in response && response.cancelled) {
-						resolve(undefined);
-					} else if ("value" in response) {
-						resolve(response.value);
-					} else {
-						resolve(undefined);
-					}
-				},
-				reject,
-			});
-			this.output({
-				type: "extension_ui_request",
-				id,
-				method: "editor",
-				title,
-				prefill,
-			} as RpcExtensionUIRequest);
-			return promise;
+		async editor(
+			title: string,
+			prefill?: string,
+			dialogOptions?: ExtensionUIDialogOptions,
+			editorOptions?: { promptStyle?: boolean },
+		): Promise<string | undefined> {
+			return requestRpcEditor(this.pendingRequests, this.output, title, prefill, dialogOptions, editorOptions);
 		}
 
 		get theme(): Theme {
@@ -356,6 +404,7 @@ export async function runRpcMode(session: AgentSession): Promise<never> {
 			// ExtensionContextActions
 			{
 				getModel: () => session.agent.state.model,
+				getSearchDb: () => session.searchDb,
 				isIdle: () => !session.isStreaming,
 				abort: () => session.abort(),
 				hasPendingMessages: () => session.queuedMessageCount > 0,

package/src/modes/rpc/rpc-types.ts

@@ -194,7 +194,15 @@ export type RpcExtensionUIRequest =
 			placeholder?: string;
 			timeout?: number;
 	  }
-	| { type: "extension_ui_request"; id: string; method: "editor"; title: string; prefill?: string }
+	| {
+			type: "extension_ui_request";
+			id: string;
+			method: "editor";
+			title: string;
+			prefill?: string;
+			promptStyle?: boolean;
+	  }
+	| { type: "extension_ui_request"; id: string; method: "cancel"; targetId: string }
 	| {
 			type: "extension_ui_request";
 			id: string;

package/src/modes/theme/theme.ts

@@ -955,6 +955,76 @@ export type ThemeColor =
 	| "statusLineCost"
 	| "statusLineSubagents";
 
+/** Set of all valid ThemeColor string values for runtime validation */
+const THEME_COLOR_RECORD = {
+	accent: true,
+	border: true,
+	borderAccent: true,
+	borderMuted: true,
+	success: true,
+	error: true,
+	warning: true,
+	muted: true,
+	dim: true,
+	text: true,
+	thinkingText: true,
+	userMessageText: true,
+	customMessageText: true,
+	customMessageLabel: true,
+	toolTitle: true,
+	toolOutput: true,
+	mdHeading: true,
+	mdLink: true,
+	mdLinkUrl: true,
+	mdCode: true,
+	mdCodeBlock: true,
+	mdCodeBlockBorder: true,
+	mdQuote: true,
+	mdQuoteBorder: true,
+	mdHr: true,
+	mdListBullet: true,
+	toolDiffAdded: true,
+	toolDiffRemoved: true,
+	toolDiffContext: true,
+	syntaxComment: true,
+	syntaxKeyword: true,
+	syntaxFunction: true,
+	syntaxVariable: true,
+	syntaxString: true,
+	syntaxNumber: true,
+	syntaxType: true,
+	syntaxOperator: true,
+	syntaxPunctuation: true,
+	thinkingOff: true,
+	thinkingMinimal: true,
+	thinkingLow: true,
+	thinkingMedium: true,
+	thinkingHigh: true,
+	thinkingXhigh: true,
+	bashMode: true,
+	pythonMode: true,
+	statusLineSep: true,
+	statusLineModel: true,
+	statusLinePath: true,
+	statusLineGitClean: true,
+	statusLineGitDirty: true,
+	statusLineContext: true,
+	statusLineSpend: true,
+	statusLineStaged: true,
+	statusLineDirty: true,
+	statusLineUntracked: true,
+	statusLineOutput: true,
+	statusLineCost: true,
+	statusLineSubagents: true,
+} satisfies Record<ThemeColor, true>;
+
+const VALID_THEME_COLORS: ReadonlySet<string> = new Set(Object.keys(THEME_COLOR_RECORD));
+
+/** Check if a string is a valid ThemeColor value */
+export function isValidThemeColor(color: string): color is ThemeColor {
+	return VALID_THEME_COLORS.has(color);
+}
+
 export type ThemeBg =
 	| "selectedBg"
 	| "userMessageBg"

package/src/modes/types.ts

@@ -243,7 +243,12 @@ export interface InteractiveModeContext {
 	hideHookSelector(): void;
 	showHookInput(title: string, placeholder?: string): Promise<string | undefined>;
 	hideHookInput(): void;
-	showHookEditor(title: string, prefill?: string): Promise<string | undefined>;
+	showHookEditor(
+		title: string,
+		prefill?: string,
+		dialogOptions?: ExtensionUIDialogOptions,
+		editorOptions?: { promptStyle?: boolean },
+	): Promise<string | undefined>;
 	hideHookEditor(): void;
 	showHookNotify(message: string, type?: "info" | "warning" | "error"): void;
 	showHookCustom<T>(

package/src/prompts/system/custom-system-prompt.md

@@ -40,6 +40,11 @@ If a skill covers your output, you **MUST** read `skill://<name>` before proceed
 {{/list}}
 </skills>
 {{/if}}
+{{#if alwaysApplyRules.length}}
+{{#each alwaysApplyRules}}
+{{content}}
+{{/each}}
+{{/if}}
 {{#if rules.length}}
 Rules are local constraints.
 You **MUST** read `rule://<name>` when working in that domain.

package/src/prompts/system/system-prompt.md

@@ -124,6 +124,12 @@ You **MUST** use the following skills, to save you time, when working in their d
 {{/each}}
 {{/if}}
 
+{{#if alwaysApplyRules.length}}
+{{#each alwaysApplyRules}}
+{{content}}
+{{/each}}
+{{/if}}
+
 {{#if rules.length}}
 # Rules
 Domain-specific rules from past experience. **MUST** read `rule://<name>` when working in their territory.

package/src/prompts/tools/ask.md

@@ -8,6 +8,7 @@ Asks user when you need clarification or input during task execution.
 - Use `recommended: <index>` to mark default (0-indexed); " (Recommended)" added automatically
 - Use `questions` for multiple related questions instead of asking one at a time
 - Set `multi: true` on question to allow multiple selections
+- `ask.timeout` only applies while choosing options; once the user selects "Other (type your own)", there is no timeout
 </instruction>
 
 <caution>

package/src/prompts/tools/grep.md

@@ -1,4 +1,4 @@
-Searches files using powerful regex matching built on ripgrep.
+Searches files using powerful regex matching.
 
 <instruction>
 - Supports full regex syntax (e.g., `log.*Error`, `function\\s+\\w+`); literal braces need escaping (`interface\\{\\}` for `interface{}` in Go)

package/src/prompts/tools/hashline.md

@@ -2,8 +2,6 @@ Applies precise file edits using `LINE#ID` anchors from `read` output.
 
 Read the file first. Copy anchors exactly from the latest `read` output. In one `edit` call, batch all edits for one file. After any successful edit, re-read before editing that file again.
 
-This matters: your output is checked against the real file state. Invalid anchors, duplicated boundary lines, or semantically equivalent rewrites will fail.
-
 <operations>
 **Top level**
 - `path` — file path
@@ -61,6 +59,24 @@ Replace only the catch body. Do not target the shared boundary line `} catch (er
 ```
 </example>
 
+<example name="replace whole block including closing brace">
+Replace the entire body of `alpha`, including its closing `}`. `end` **MUST** be {{hlineref 7 "}"}} because `content` includes `}`.
+```
+{
+  path: "util.ts",
+  edits: [{
+    loc: { block: { pos: {{hlineref 6 "\tlog();"}}, end: {{hlineref 7 "}"}} } },
+    content: [
+      "\tvalidate();",
+      "\tlog();",
+      "}"
+    ]
+  }]
+}
+```
+**Wrong**: using `end: {{hlineref 6 "\tlog();"}}` with the same content — line 7 (`}`) survives the replacement AND content emits `}`, producing two closing braces.
+</example>
+
 <example name="replace one line">
 ```
 {
@@ -108,9 +124,8 @@ When adding a sibling declaration, prefer `prepend` on the next declaration.
 - Make the minimum exact edit. Do not rewrite nearby code unless the consumed range requires it.
 - Use anchors exactly as `N#ID` from the latest `read` output.
 - `block` requires both `pos` and `end`. Other anchored ops require one anchor.
-- Replace exactly the owned span. If `content` re-emits content beyond `end`, it will duplicate.
-- **Boundary duplication trap**: when replacing a block, `end` must be the **last line of the block** (e.g. the closing `}`), not the last *content* line before it. Otherwise the closing delimiter survives and your replacement adds a second copy.
-- Do not target shared boundary lines such as `} else {`, `} catch (…) {`, `}),`, or `},{`.
+- When your replacement `content` ends with a closing delimiter (`}`, `*/`, `)`, `]`), verify `end` includes the original line carrying that delimiter. If `end` stops one line too early, the original delimiter survives and your content adds a second copy.
+- **Self-check**: compare the last line of `content` with the line immediately after `end` in the file. If they match (e.g., both are `}`), extend `end` to include that line.
 - For a block, either replace only the body or replace the whole block. Do not split block boundaries.
 - `content` must be literal file content with matching indentation. If the file uses tabs, use real tabs.
 - Do not use this tool to reformat or clean up unrelated code.

package/src/sdk.ts

@@ -9,8 +9,17 @@ import {
 import type { Message, Model } from "@oh-my-pi/pi-ai";
 
 import { prewarmOpenAICodexResponses } from "@oh-my-pi/pi-ai/providers/openai-codex-responses";
+import { SearchDb } from "@oh-my-pi/pi-natives";
 import type { Component } from "@oh-my-pi/pi-tui";
-import { $env, getAgentDbPath, getAgentDir, getProjectDir, logger, postmortem } from "@oh-my-pi/pi-utils";
+import {
+	$env,
+	getAgentDbPath,
+	getAgentDir,
+	getProjectDir,
+	getSearchDbDir,
+	logger,
+	postmortem,
+} from "@oh-my-pi/pi-utils";
 import chalk from "chalk";
 import { AsyncJobManager } from "./async";
 import { createAutoresearchExtension } from "./autoresearch";
@@ -131,6 +140,8 @@ export interface CreateAgentSessionOptions {
 	authStorage?: AuthStorage;
 	/** Model registry. Default: discoverModels(authStorage, agentDir) */
 	modelRegistry?: ModelRegistry;
+	/** Shared native search DB for grep/glob/fuzzyFind-backed workflows. */
+	searchDb?: SearchDb;
 
 	/** Model to use. Default: from settings, else first available */
 	model?: Model;
@@ -381,6 +392,7 @@ function createCustomToolContext(ctx: ExtensionContext): CustomToolContext {
 		sessionManager: ctx.sessionManager,
 		modelRegistry: ctx.modelRegistry,
 		model: ctx.model,
+		searchDb: ctx.searchDb,
 		isIdle: ctx.isIdle,
 		hasQueuedMessages: ctx.hasPendingMessages,
 		abort: ctx.abort,
@@ -796,6 +808,12 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		}),
 	);
 
+	// collect alwaysApply rules — full content injected into system prompt
+	const alwaysApplyRules = rulesResult.items.filter((rule: Rule) => {
+		if (registeredTtsrRuleNames.has(rule.name)) return false;
+		return rule.alwaysApply === true;
+	});
+
 	const contextFiles = await logger.timeAsync(
 		"discoverContextFiles",
 		async () => options.contextFiles ?? (await discoverContextFiles(cwd, agentDir)),
@@ -856,6 +874,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 			})
 		: undefined;
 
+	const searchDb = options.searchDb ?? new SearchDb(getSearchDbDir(agentDir));
 	const pendingActionStore = new PendingActionStore();
 	const toolSession: ToolSession = {
 		cwd,
@@ -905,6 +924,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		modelRegistry,
 		asyncJobManager,
 		pendingActionStore,
+		searchDb,
 	};
 
 	// Initialize internal URL router for internal protocols (agent://, artifact://, memory://, skill://, rule://, mcp://, local://)
@@ -930,7 +950,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 	);
 	internalRouter.register(
 		new RuleProtocolHandler({
-			getRules: () => rulebookRules,
+			getRules: () => [...rulebookRules, ...alwaysApplyRules],
 		}),
 	);
 	internalRouter.register(new PiProtocolHandler());
@@ -1167,6 +1187,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 			sessionManager,
 			modelRegistry,
 			model: agent?.state.model,
+			searchDb,
 			isIdle: () => !session?.isStreaming,
 			hasQueuedMessages: () => (session?.queuedMessageCount ?? 0) > 0,
 			abort: () => session?.abort(),
@@ -1252,6 +1273,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 			tools: promptTools,
 			toolNames,
 			rules: rulebookRules,
+			alwaysApplyRules,
 			skillsSettings: settings.getGroup("skills"),
 			appendSystemPrompt: appendPrompt,
 			repeatToolDescriptions,
@@ -1272,6 +1294,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 				tools: promptTools,
 				toolNames,
 				rules: rulebookRules,
+				alwaysApplyRules,
 				skillsSettings: settings.getGroup("skills"),
 				customPrompt: options.systemPrompt,
 				appendSystemPrompt: appendPrompt,
@@ -1531,6 +1554,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		obfuscator,
 		asyncJobManager,
 		pendingActionStore,
+		searchDb,
 	});
 
 	if (model?.api === "openai-codex-responses") {

package/src/session/agent-session.ts

@@ -50,10 +50,11 @@ import {
 	modelsAreEqual,
 	parseRateLimitReason,
 } from "@oh-my-pi/pi-ai";
+import type { SearchDb } from "@oh-my-pi/pi-natives";
 import { abortableSleep, getAgentDbPath, isEnoent, logger } from "@oh-my-pi/pi-utils";
 import type { AsyncJob, AsyncJobManager } from "../async";
 import type { Rule } from "../capability/rule";
-import { MODEL_ROLE_IDS, type ModelRegistry, type ModelRole } from "../config/model-registry";
+import { MODEL_ROLE_IDS, type ModelRegistry } from "../config/model-registry";
 import { extractExplicitThinkingSelector, parseModelString, resolveModelRoleValue } from "../config/model-resolver";
 import { expandPromptTemplate, type PromptTemplate, renderPromptTemplate } from "../config/prompt-templates";
 import type { Settings, SkillsSettings } from "../config/settings";
@@ -237,6 +238,8 @@ export interface AgentSessionConfig {
 	obfuscator?: SecretObfuscator;
 	/** Pending action store for preview/apply workflows */
 	pendingActionStore?: PendingActionStore;
+	/** Shared native search DB for grep/glob/fuzzyFind-backed workflows. */
+	searchDb?: SearchDb;
 }
 
 /** Options for AgentSession.prompt() */
@@ -269,7 +272,7 @@ export interface ModelCycleResult {
 export interface RoleModelCycleResult {
 	model: Model;
 	thinkingLevel: ThinkingLevel | undefined;
-	role: ModelRole;
+	role: string;
 }
 
 /** Session statistics for /session command */
@@ -348,6 +351,7 @@ export class AgentSession {
 	readonly agent: Agent;
 	readonly sessionManager: SessionManager;
 	readonly settings: Settings;
+	readonly searchDb: SearchDb | undefined;
 
 	#asyncJobManager: AsyncJobManager | undefined = undefined;
 	#scopedModels: Array<{ model: Model; thinkingLevel?: ThinkingLevel }>;
@@ -462,6 +466,7 @@ export class AgentSession {
 		this.agent = config.agent;
 		this.sessionManager = config.sessionManager;
 		this.settings = config.settings;
+		this.searchDb = config.searchDb;
 		this.#asyncJobManager = config.asyncJobManager;
 		this.#scopedModels = config.scopedModels ?? [];
 		this.#thinkingLevel = config.thinkingLevel;
@@ -1888,6 +1893,7 @@ export class AgentSession {
 			sessionManager: this.sessionManager,
 			modelRegistry: this.#modelRegistry,
 			model: this.model,
+			searchDb: this.searchDb,
 			isIdle: () => !this.isStreaming,
 			hasQueuedMessages: () => this.queuedMessageCount > 0,
 			abort: () => {
@@ -2039,7 +2045,7 @@ export class AgentSession {
 		);
 	}
 
-	resolveRoleModel(role: ModelRole): Model | undefined {
+	resolveRoleModel(role: string): Model | undefined {
 		return this.#resolveRoleModel(role, this.#modelRegistry.getAvailable(), this.model);
 	}
 
@@ -3096,7 +3102,7 @@ export class AgentSession {
 	 * Validates API key, saves to session and settings.
 	 * @throws Error if no API key available for the model
 	 */
-	async setModel(model: Model, role: ModelRole = "default"): Promise<void> {
+	async setModel(model: Model, role: string = "default"): Promise<void> {
 		const apiKey = await this.#modelRegistry.getApiKey(model, this.sessionId);
 		if (!apiKey) {
 			throw new Error(`No API key for ${model.provider}/${model.id}`);
@@ -3150,7 +3156,7 @@ export class AgentSession {
 	 * @param options - Optional settings: `temporary` to not persist to settings
 	 */
 	async cycleRoleModels(
-		roleOrder: readonly ModelRole[],
+		roleOrder: readonly string[],
 		options?: { temporary?: boolean },
 	): Promise<RoleModelCycleResult | undefined> {
 		const availableModels = this.#modelRegistry.getAvailable();
@@ -3160,7 +3166,7 @@ export class AgentSession {
 		if (!currentModel) return undefined;
 		const matchPreferences = { usageOrder: this.settings.getStorage()?.getModelUsageOrder() };
 		const roleModels: Array<{
-			role: ModelRole;
+			role: string;
 			model: Model;
 			thinkingLevel?: ThinkingLevel;
 			explicitThinkingLevel: boolean;
@@ -3190,9 +3196,10 @@ export class AgentSession {
 		if (roleModels.length <= 1) return undefined;
 
 		const lastRole = this.sessionManager.getLastModelChangeRole();
-		let currentIndex = lastRole
-			? roleModels.findIndex(entry => entry.role === lastRole)
-			: roleModels.findIndex(entry => modelsAreEqual(entry.model, currentModel));
+		let currentIndex = lastRole ? roleModels.findIndex(entry => entry.role === lastRole) : -1;
+		if (currentIndex === -1) {
+			currentIndex = roleModels.findIndex(entry => modelsAreEqual(entry.model, currentModel));
+		}
 		if (currentIndex === -1) currentIndex = 0;
 
 		const nextIndex = (currentIndex + 1) % roleModels.length;
@@ -4273,7 +4280,7 @@ export class AgentSession {
 		return `${model.provider}/${model.id}`;
 	}
 
-	#formatRoleModelValue(role: ModelRole, model: Model): string {
+	#formatRoleModelValue(role: string, model: Model): string {
 		const modelKey = `${model.provider}/${model.id}`;
 		const existingRoleValue = this.settings.getModelRole(role);
 		if (!existingRoleValue) return modelKey;
@@ -4295,7 +4302,7 @@ export class AgentSession {
 		return availableModels.find(m => m.provider === currentModel.provider && m.id === configuredTarget);
 	}
 
-	#resolveRoleModel(role: ModelRole, availableModels: Model[], currentModel: Model | undefined): Model | undefined {
+	#resolveRoleModel(role: string, availableModels: Model[], currentModel: Model | undefined): Model | undefined {
 		const roleModelStr =
 			role === "default"
 				? (this.settings.getModelRole("default") ??

package/src/system-prompt.ts

@@ -16,6 +16,57 @@ import { type ContextFile, loadCapability, type SystemPrompt as SystemPromptFile
 import { loadSkills, type Skill } from "./extensibility/skills";
 import customSystemPromptTemplate from "./prompts/system/custom-system-prompt.md" with { type: "text" };
 import systemPromptTemplate from "./prompts/system/system-prompt.md" with { type: "text" };
+import { formatPromptContent } from "./utils/prompt-format";
+
+interface AlwaysApplyRule {
+	name: string;
+	content: string;
+	path: string;
+}
+
+function normalizePromptBlock(content: string): string {
+	return formatPromptContent(content, { renderPhase: "post-render" }).trim();
+}
+
+function splitComparablePromptBlocks(content: string | null | undefined): string[] {
+	const normalized = firstNonEmpty(content);
+	if (!normalized) return [];
+
+	return normalizePromptBlock(normalized)
+		.split(/\n{2,}/)
+		.map(block => block.trim())
+		.filter(block => block.length > 0);
+}
+
+function promptSourceContainsRule(source: string | null | undefined, ruleContent: string): boolean {
+	const sourceBlocks = splitComparablePromptBlocks(source);
+	const ruleBlocks = splitComparablePromptBlocks(ruleContent);
+	if (sourceBlocks.length === 0 || ruleBlocks.length === 0 || ruleBlocks.length > sourceBlocks.length) return false;
+
+	for (let start = 0; start <= sourceBlocks.length - ruleBlocks.length; start += 1) {
+		if (ruleBlocks.every((block, offset) => sourceBlocks[start + offset] === block)) return true;
+	}
+
+	return false;
+}
+
+function dedupeAlwaysApplyRules(
+	alwaysApplyRules: AlwaysApplyRule[] | undefined,
+	promptSources: Array<string | null | undefined>,
+): AlwaysApplyRule[] {
+	if (!alwaysApplyRules || alwaysApplyRules.length === 0) return [];
+
+	return alwaysApplyRules.filter(
+		rule => !promptSources.some(source => promptSourceContainsRule(source, rule.content)),
+	);
+}
+
+function dedupePromptSource(source: string | null | undefined, otherSources: Array<string | null | undefined>): string {
+	const resolvedSource = firstNonEmpty(source);
+	if (!resolvedSource) return "";
+
+	return otherSources.some(otherSource => promptSourceContainsRule(otherSource, resolvedSource)) ? "" : resolvedSource;
+}
 
 function firstNonEmpty(...values: (string | undefined | null)[]): string | null {
 	for (const value of values) {
@@ -379,6 +430,8 @@ export interface BuildSystemPromptOptions {
 	mcpDiscoveryServerSummaries?: string[];
 	/** Encourage the agent to delegate via tasks unless changes are trivial. */
 	eagerTasks?: boolean;
+	/** Rules with alwaysApply=true — their full content is injected into the prompt. */
+	alwaysApplyRules?: AlwaysApplyRule[];
 }
 
 /** Build the system prompt with tools, guidelines, and context */
@@ -398,6 +451,7 @@ export async function buildSystemPrompt(options: BuildSystemPromptOptions = {}):
 		contextFiles: providedContextFiles,
 		skills: providedSkills,
 		rules,
+		alwaysApplyRules,
 		intentField,
 		mcpDiscoveryMode = false,
 		mcpDiscoveryServerSummaries = [],
@@ -519,10 +573,16 @@ export async function buildSystemPrompt(options: BuildSystemPromptOptions = {}):
 	const hasRead = tools?.has("read");
 	const filteredSkills = hasRead ? skills : [];
 
+	const effectiveSystemPromptCustomization = dedupePromptSource(systemPromptCustomization, [
+		resolvedCustomPrompt,
+		resolvedAppendPrompt,
+	]);
+	const promptSources = [effectiveSystemPromptCustomization, resolvedCustomPrompt, resolvedAppendPrompt];
+	const injectedAlwaysApplyRules = dedupeAlwaysApplyRules(alwaysApplyRules, promptSources);
+
 	const environment = await logger.timeAsync("getEnvironmentInfo", getEnvironmentInfo);
 	const data = {
-		// Explicit custom prompts replace discovered SYSTEM.md content rather than layering it twice.
-		systemPromptCustomization: resolvedCustomPrompt ? "" : (systemPromptCustomization ?? ""),
+		systemPromptCustomization: effectiveSystemPromptCustomization,
 		customPrompt: resolvedCustomPrompt,
 		appendPrompt: resolvedAppendPrompt ?? "",
 		tools: toolNames,
@@ -533,6 +593,7 @@ export async function buildSystemPrompt(options: BuildSystemPromptOptions = {}):
 		agentsMdSearch,
 		skills: filteredSkills,
 		rules: rules ?? [],
+		alwaysApplyRules: injectedAlwaysApplyRules,
 		date,
 		dateTime,
 		cwd: promptCwd,