diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index 8d165f70b..b55c0720e 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -1,7 +1,6 @@
 # Changelog
 
 ## [Unreleased]
-
 ### Breaking Changes
 
 - Changed hashline edit schema from flat `op`/`pos`/`end`/`lines` fields to structured `loc`/`content` format with location-specific objects
@@ -14,6 +13,14 @@
 
 ### Added
 
+- Added prompt for tradeoff metrics during autoresearch setup to collect secondary metrics alongside primary metric
+- Added validation of contract path specifications to reject absolute paths and parent directory references
+- Added stricter benchmark command validation in `isAutoresearchShCommand()` to reject chained commands, pipes, and redirects
+- Added protection against prototype pollution in ASI data and metric cloning by filtering `__proto__`, `constructor`, and `prototype` keys
+- Added `autoResumeArmed` flag to track when autoresearch should automatically resume pending runs
+- Added `lastAutoResumePendingRunNumber` to prevent duplicate auto-resume prompts for the same pending run
+- Added `git clean -X` invocation during failed experiment rollback to remove ignored build artifacts
+- Added validation to reject `init_experiment` when a previous run is still pending and unlogged
 - Added autoresearch contract system for validating benchmark commands, metrics, scope paths, off-limits paths, and constraints with fingerprint tracking to detect configuration drift
 - Added `autoresearch.program.md` support for repo-local playbook overlays that guide session strategy while preserving `autoresearch.md` as source of truth
 - Added pending run artifact tracking and recovery to resume incomplete experiments from `.autoresearch/runs/` directory with run numbers and benchmark logs
@@ -62,6 +69,19 @@
 
 ### Changed
 
+- Changed `isAutoresearchShCommand()` to use proper command-line argument parsing instead of regex, improving accuracy for complex shell invocations
+- Changed autoresearch initialization prompt to display collected tradeoff metrics in the setup summary
+- Changed `command-initialize.md` template to include guidance on preflight requirements, comparability invariants, and marking measurement-critical files as off-limits
+- Changed `command-initialize.md` to instruct users to write or update `autoresearch.program.md` with durable heuristics and repo-specific strategy
+- Changed autoresearch resume guidance to emphasize continuing on the current protected branch rather than switching branches
+- Changed autoresearch prompt to clarify that `autoresearch.md` holds durable conclusions while `autoresearch.ideas.md` is the scratch backlog
+- Changed autoresearch prompt guidance to require stable measurement harness and fixed benchmark inputs unless intentionally starting a new segment
+- Changed autoresearch prompt to recommend keeping equal or near-equal results when they materially simplify implementation
+- Changed `init_experiment` to reset pending run state (checks, duration, ASI, artifact directory) when initializing a new segment
+- Changed `log_experiment` to set `autoResumeArmed` flag after successfully logging a run to enable auto-resume on next agent turn
+- Changed `run_experiment` to set `autoResumeArmed` flag and update dashboard after completing a run
+- Changed auto-resume logic to only prompt when a new pending run exists or when `autoResumeArmed` is explicitly set, preventing duplicate prompts
+- Changed path normalization in contract validation to use `path.posix.normalize()` for consistent path handling
 - Changed autoresearch initialization to collect and validate benchmark command, metric definition, scope paths, off-limits list, and constraints before `init_experiment`
 - Changed `init_experiment` to require exact benchmark command, metric definition, scope, off-limits, and constraints matching collected contract
 - Changed `log_experiment` to record run number, benchmark command, scope paths, off-limits list, constraints, and segment fingerprint with each result
@@ -111,6 +131,9 @@
 
 ### Fixed
 
+- Fixed boundary duplication warnings to always display when replacement lines match the next surviving line, even when auto-correction is disabled
+- Fixed secondary metrics validation to properly reject missing configured metrics and new metrics without force flag
+- Fixed ASI data cloning to prevent prototype pollution attacks by filtering reserved property names
 - Fixed autoresearch resume to detect and recover pending run artifacts that were left unlogged from previous sessions
 - Fixed dashboard overlay to display when running experiment even with zero completed results
 - Fixed tab character rendering in dashboard command display and tool output summaries
diff --git a/packages/coding-agent/src/autoresearch/command-initialize.md b/packages/coding-agent/src/autoresearch/command-initialize.md
index 9986a844b..1e7939d42 100644
--- a/packages/coding-agent/src/autoresearch/command-initialize.md
+++ b/packages/coding-agent/src/autoresearch/command-initialize.md
@@ -10,6 +10,8 @@ Collected setup:
 - primary metric: `{{metric_name}}`
 - metric unit: `{{metric_unit}}`
 - direction: `{{direction}}`
+- tradeoff metrics:
+{{{secondary_metrics_block}}}
 - files in scope:
 {{{scope_paths_block}}}
 - off limits:
@@ -21,8 +23,10 @@ Explain briefly what autoresearch will do in this repository, then initialize th
 
 Your first actions:
 - write `autoresearch.md`
-- record the collected benchmark command, primary metric, metric unit, direction, scope, off-limits list, and constraints in `autoresearch.md`
-- optionally write `autoresearch.program.md` when a repo-local playbook would help future resume quality
+- record the collected benchmark command, primary metric, metric unit, direction, tradeoff metrics, scope, off-limits list, and constraints in `autoresearch.md`
+- add a short preflight section in `autoresearch.md` covering prerequisites, one-time setup, and the comparability invariant that must stay fixed across runs
+- explicitly mark the ground-truth evaluator, fixed datasets, and other measurement-critical files as off-limits or hard constraints when they define the benchmark contract
+- write or update `autoresearch.program.md` when you learn durable heuristics, failure patterns, or repo-specific strategy that future resume turns should inherit
 - define the benchmark entrypoint in `autoresearch.sh`
 - optionally add `autoresearch.checks.sh` if correctness or quality needs a hard gate
 - run `init_experiment` with the exact collected benchmark command, metric definition, scope paths, off-limits list, and constraints
diff --git a/packages/coding-agent/src/autoresearch/command-resume.md b/packages/coding-agent/src/autoresearch/command-resume.md
index 3dd0030a4..e71543cb1 100644
--- a/packages/coding-agent/src/autoresearch/command-resume.md
+++ b/packages/coding-agent/src/autoresearch/command-resume.md
@@ -13,5 +13,5 @@ Additional context from the user:
 Use the notes as the source of truth for the current direction, scope, and constraints.
 - inspect recent git history for context
 - inspect `autoresearch.jsonl` if it exists
-- continue the most promising unfinished branch
+- continue the most promising unfinished direction on the current protected branch
 - keep iterating until interrupted or until the configured iteration cap is reached
diff --git a/packages/coding-agent/src/autoresearch/contract.ts b/packages/coding-agent/src/autoresearch/contract.ts
index 45d4c4e46..c5b8b87c9 100644
--- a/packages/coding-agent/src/autoresearch/contract.ts
+++ b/packages/coding-agent/src/autoresearch/contract.ts
@@ -63,6 +63,16 @@ export function validateAutoresearchContract(contract: AutoresearchContract): st
 	if (contract.scopePaths.length === 0) {
 		errors.push("Files in Scope must contain at least one path in autoresearch.md.");
 	}
+	for (const scopePath of contract.scopePaths) {
+		if (isUnsafeContractPathSpec(scopePath)) {
+			errors.push(`Files in Scope contains an invalid path: ${scopePath}`);
+		}
+	}
+	for (const offLimitsPath of contract.offLimits) {
+		if (isUnsafeContractPathSpec(offLimitsPath)) {
+			errors.push(`Off Limits contains an invalid path: ${offLimitsPath}`);
+		}
+	}
 	return errors;
 }
 
@@ -151,7 +161,7 @@ export function normalizeAutoresearchList(values: readonly string[]): string[] {
 }
 
 export function normalizeContractPathSpec(value: string): string {
-	const normalized = value.trim().replaceAll("\\", "/");
+	const normalized = path.posix.normalize(value.trim().replaceAll("\\", "/"));
 	if (normalized === "." || normalized === "./") return ".";
 	return normalized.replace(/^\.\/+/, "").replace(/\/+$/, "");
 }
@@ -316,3 +326,7 @@ function parseSecondaryMetrics(value: string | undefined): string[] {
 			.filter(Boolean),
 	);
 }
+
+function isUnsafeContractPathSpec(value: string): boolean {
+	return path.posix.isAbsolute(value) || value === ".." || value.startsWith("../");
+}
diff --git a/packages/coding-agent/src/autoresearch/helpers.ts b/packages/coding-agent/src/autoresearch/helpers.ts
index 20f2ae0f7..e278d3631 100644
--- a/packages/coding-agent/src/autoresearch/helpers.ts
+++ b/packages/coding-agent/src/autoresearch/helpers.ts
@@ -1,6 +1,7 @@
 import * as fs from "node:fs";
 import * as path from "node:path";
 import { isEnoent } from "@oh-my-pi/pi-utils";
+import { parseCommandArgs } from "../utils/command-args";
 import type {
 	ASIData,
 	ASIValue,
@@ -185,8 +186,36 @@ export function isAutoresearchShCommand(command: string): boolean {
 		previous = normalized;
 		normalized = normalized.replace(/^(?:env|time|nice|nohup)(?:\s+-\S+(?:\s+\d+)?)?\s+/, "");
 	}
+	if (/[;&|<>]/.test(normalized)) {
+		return false;
+	}
 
-	return /^(?:(?:bash|sh)\s+(?:-\w+\s+)*)?(?:\.\/|\/[\w/.-]*\/)?autoresearch\.sh(?:\s|$)/.test(normalized);
+	const tokens = parseCommandArgs(normalized);
+	if (tokens.length === 0) return false;
+
+	let index = 0;
+	if (tokens[index] === "bash" || tokens[index] === "sh") {
+		index += 1;
+		while (index < tokens.length && tokens[index]?.startsWith("-")) {
+			if (tokens[index]?.includes("c")) {
+				return false;
+			}
+			index += 1;
+		}
+	}
+
+	const scriptToken = tokens[index];
+	if (!scriptToken || !/^(?:\.\/|\/[\w/.-]*\/)?autoresearch\.sh$/.test(scriptToken)) {
+		return false;
+	}
+
+	for (const token of tokens.slice(index + 1)) {
+		if (token === "&&" || token === "||" || token === ";" || token === "|" || token === ">" || token === "<") {
+			return false;
+		}
+	}
+
+	return true;
 }
 
 export function isBetter(current: number, best: number, direction: MetricDirection): boolean {
@@ -380,6 +409,7 @@ function cloneNumericMetricMap(value: unknown): NumericMetricMap | null {
 	const metrics = value as { [key: string]: unknown };
 	const clone: NumericMetricMap = {};
 	for (const [key, entryValue] of Object.entries(metrics)) {
+		if (DENIED_KEY_NAMES.has(key)) continue;
 		if (typeof entryValue === "number" && Number.isFinite(entryValue)) {
 			clone[key] = entryValue;
 		}
@@ -392,6 +422,7 @@ function cloneAsiData(value: unknown): ASIData | null {
 	const candidate = value as { [key: string]: unknown };
 	const clone: ASIData = {};
 	for (const [key, entryValue] of Object.entries(candidate)) {
+		if (DENIED_KEY_NAMES.has(key)) continue;
 		const sanitized = clonePendingAsiValue(entryValue);
 		if (sanitized !== undefined) {
 			clone[key] = sanitized;
@@ -415,6 +446,7 @@ function clonePendingAsiValue(value: unknown): ASIValue | undefined {
 		const candidate = value as { [key: string]: unknown };
 		const clone: { [key: string]: ASIValue } = {};
 		for (const [key, entryValue] of Object.entries(candidate)) {
+			if (DENIED_KEY_NAMES.has(key)) continue;
 			const sanitized = clonePendingAsiValue(entryValue);
 			if (sanitized !== undefined) {
 				clone[key] = sanitized;
diff --git a/packages/coding-agent/src/autoresearch/index.ts b/packages/coding-agent/src/autoresearch/index.ts
index 4ddcbd2c2..8173b12d3 100644
--- a/packages/coding-agent/src/autoresearch/index.ts
+++ b/packages/coding-agent/src/autoresearch/index.ts
@@ -43,6 +43,7 @@ interface AutoresearchSetupInput {
 	metricName: string;
 	metricUnit: string;
 	direction: "lower" | "higher";
+	secondaryMetrics: string[];
 	scopePaths: string[];
 	offLimits: string[];
 	constraints: string[];
@@ -65,6 +66,8 @@ export const createAutoresearchExtension: ExtensionFactory = api => {
 		runtime.state.maxExperiments = readMaxExperiments(ctx.cwd);
 		runtime.goal = control.goal;
 		runtime.autoresearchMode = control.autoresearchMode;
+		runtime.autoResumeArmed = false;
+		runtime.lastAutoResumePendingRunNumber = null;
 		runtime.lastRunSummary = await readPendingRunSummary(workDir, loggedRunNumbers);
 		runtime.lastRunChecks = summaryToChecks(runtime.lastRunSummary);
 		runtime.lastRunDuration = runtime.lastRunSummary?.durationSeconds ?? null;
@@ -94,7 +97,9 @@ export const createAutoresearchExtension: ExtensionFactory = api => {
 	): void => {
 		const runtime = getRuntime(ctx);
 		runtime.autoresearchMode = enabled;
+		runtime.autoResumeArmed = false;
 		runtime.goal = goal;
+		runtime.lastAutoResumePendingRunNumber = null;
 		api.appendEntry("autoresearch-control", goal ? { mode, goal } : { mode });
 	};
 
@@ -251,6 +256,7 @@ export const createAutoresearchExtension: ExtensionFactory = api => {
 			runtime.state.metricName = setup.metricName;
 			runtime.state.metricUnit = setup.metricUnit;
 			runtime.state.bestDirection = setup.direction;
+			runtime.state.secondaryMetrics = setup.secondaryMetrics.map(name => ({ name, unit: "" }));
 			runtime.state.benchmarkCommand = setup.benchmarkCommand;
 			runtime.state.scopePaths = [...setup.scopePaths];
 			runtime.state.offLimits = [...setup.offLimits];
@@ -267,6 +273,13 @@ export const createAutoresearchExtension: ExtensionFactory = api => {
 					metric_name: setup.metricName,
 					metric_unit: setup.metricUnit,
 					direction: setup.direction,
+					has_secondary_metrics: setup.secondaryMetrics.length > 0,
+					secondary_metrics: setup.secondaryMetrics,
+					secondary_metrics_block: formatBulletBlock(
+						setup.secondaryMetrics,
+						value => `  - \`${value}\``,
+						"  - `(none)`",
+					),
 					scope_paths: setup.scopePaths,
 					scope_paths_block: formatBulletBlock(setup.scopePaths, value => `  - \`${value}\``),
 					has_off_limits: setup.offLimits.length > 0,
@@ -315,7 +328,10 @@ export const createAutoresearchExtension: ExtensionFactory = api => {
 		dashboard.updateWidget(ctx, runtime);
 		dashboard.requestRender();
 		if (!runtime.autoresearchMode) return;
-		if (ctx.hasPendingMessages()) return;
+		if (ctx.hasPendingMessages()) {
+			runtime.autoResumeArmed = false;
+			return;
+		}
 		const workDir = resolveWorkDir(ctx.cwd);
 		const pendingRun =
 			runtime.lastRunSummary ??
@@ -324,6 +340,13 @@ export const createAutoresearchExtension: ExtensionFactory = api => {
 		runtime.lastRunChecks = summaryToChecks(pendingRun);
 		runtime.lastRunDuration = pendingRun?.durationSeconds ?? runtime.lastRunDuration;
 		runtime.lastRunAsi = pendingRun?.parsedAsi ?? runtime.lastRunAsi;
+		const shouldResumePendingRun =
+			pendingRun !== null && runtime.lastAutoResumePendingRunNumber !== pendingRun.runNumber;
+		if (!shouldResumePendingRun && !runtime.autoResumeArmed) {
+			return;
+		}
+		runtime.autoResumeArmed = false;
+		runtime.lastAutoResumePendingRunNumber = pendingRun?.runNumber ?? null;
 		const autoresearchMdPath = path.join(workDir, "autoresearch.md");
 		const ideasPath = path.join(workDir, "autoresearch.ideas.md");
 		api.sendMessage(
@@ -459,6 +482,9 @@ async function promptForAutoresearchSetup(
 		return undefined;
 	}
 
+	const secondaryMetricsInput = await ctx.ui.input("Tradeoff Metrics", "");
+	if (secondaryMetricsInput === undefined) return undefined;
+
 	const scopePathsInput = await ctx.ui.input("Files in Scope", "packages/coding-agent/src/autoresearch");
 	if (scopePathsInput === undefined) return undefined;
 	const scopePaths = splitSetupList(scopePathsInput);
@@ -478,6 +504,7 @@ async function promptForAutoresearchSetup(
 		metricName,
 		metricUnit,
 		direction: normalizedDirection,
+		secondaryMetrics: splitSetupList(secondaryMetricsInput),
 		scopePaths,
 		offLimits: splitSetupList(offLimitsInput),
 		constraints: splitSetupList(constraintsInput),
diff --git a/packages/coding-agent/src/autoresearch/prompt.md b/packages/coding-agent/src/autoresearch/prompt.md
index c02c20f13..185edcbfe 100644
--- a/packages/coding-agent/src/autoresearch/prompt.md
+++ b/packages/coding-agent/src/autoresearch/prompt.md
@@ -71,13 +71,17 @@ An unlogged run artifact exists at `{{pending_run_directory}}`.
    - Read the relevant source files.
    - Identify the true bottleneck or quality constraint.
    - Check existing scripts, benchmark harnesses, and config files.
+   - Verify prerequisites, one-time setup, and benchmark inputs before the first run of a segment.
 2. Keep your notes in `autoresearch.md`.
-   - Record the goal, the benchmark command, the primary metric, important secondary metrics, the files in scope, hard constraints, and the running ideas backlog.
+   - Record the goal, the benchmark command, the primary metric, important secondary metrics, the files in scope, hard constraints, preflight requirements, and the benchmark comparability invariant.
    - Update the notes whenever the strategy changes.
+   - Keep durable conclusions in `autoresearch.md`.
+   - Use `autoresearch.ideas.md` for deferred experiment ideas that are promising but not active yet.
 3. Use `autoresearch.sh` as the canonical benchmark entrypoint.
    - If it does not exist yet, create it.
    - Make it print structured metric lines in the form `METRIC name=value`.
    - Use the same workload every run unless you intentionally re-initialize with a new segment.
+   - Keep the measurement harness, evaluator, and fixed benchmark inputs stable unless you intentionally start a new segment and document the change.
 4. Initialize the loop with `init_experiment` before the first logged run of a segment.
 5. Run a baseline first.
    - Establish the baseline metric before attempting optimizations.
@@ -98,7 +102,8 @@ An unlogged run artifact exists at `{{pending_run_directory}}`.
    - Use ASI to capture what you learned, not just what you changed.
 9. Prefer simpler wins.
    - Remove dead ends.
-   - Do not keep complexity that does not move the metric.
+   - Keep equal or near-equal results when they materially simplify the implementation.
+   - Do not keep ugly complexity for tiny gains unless the payoff is clearly worth it.
    - Do not thrash between unrelated ideas without writing down the conclusion.
 10. When confidence is low, confirm.
     - The dashboard confidence score compares the best observed improvement against the observed noise floor.
@@ -116,6 +121,8 @@ Your benchmark script SHOULD:
 - print secondary metrics as additional `METRIC name=value` lines
 - avoid extra randomness when possible
 - use repeated samples and median-style summaries for fast benchmarks
+- preserve the comparability invariant for the current segment
+- keep the ground-truth evaluator and fixed benchmark inputs unchanged unless the segment is explicitly re-initialized
 
 ### Notes file template
 
@@ -182,7 +189,7 @@ Resume from the existing notes:
 - read `autoresearch.md`
 - inspect recent git history
 - inspect `autoresearch.jsonl`
-- continue from the most promising unfinished branch
+- continue from the most promising unfinished direction on the current protected branch
 
 {{else}}
 ### Initial setup
@@ -215,6 +222,6 @@ Treat failing checks as a failed experiment:
 
 `autoresearch.ideas.md` exists at `{{ideas_path}}`.
 
-Use it to keep promising but deferred experiments. Prune stale ideas when they are disproven or superseded.
+Use it to keep promising but deferred experiments. `autoresearch.md` should hold durable conclusions; `autoresearch.ideas.md` is the scratch backlog. Prune stale ideas when they are disproven or superseded.
 
 {{/if}}
diff --git a/packages/coding-agent/src/autoresearch/resume-message.md b/packages/coding-agent/src/autoresearch/resume-message.md
index 64c4816f3..31052bb78 100644
--- a/packages/coding-agent/src/autoresearch/resume-message.md
+++ b/packages/coding-agent/src/autoresearch/resume-message.md
@@ -10,7 +10,7 @@ Continue the autoresearch loop now.
 {{/if}}
 - Continue from the most promising unfinished direction.
 {{#if has_ideas}}
-- Review `autoresearch.ideas.md` for promising next steps and prune stale items.
+- Review `autoresearch.ideas.md` for deferred next steps and prune stale items.
 {{/if}}
 - Keep iterating until interrupted or until the configured iteration cap is reached.
 - Preserve correctness and do not game the benchmark.
diff --git a/packages/coding-agent/src/autoresearch/state.ts b/packages/coding-agent/src/autoresearch/state.ts
index 725a60715..9ab05a60d 100644
--- a/packages/coding-agent/src/autoresearch/state.ts
+++ b/packages/coding-agent/src/autoresearch/state.ts
@@ -41,7 +41,9 @@ export function createExperimentState(): ExperimentState {
 export function createSessionRuntime(): AutoresearchRuntime {
 	return {
 		autoresearchMode: false,
+		autoResumeArmed: false,
 		dashboardExpanded: false,
+		lastAutoResumePendingRunNumber: null,
 		lastRunChecks: null,
 		lastRunDuration: null,
 		lastRunAsi: null,
@@ -341,6 +343,7 @@ function cloneNumericMetrics(value: unknown): NumericMetricMap {
 	const metrics = value as { [key: string]: unknown };
 	const clone: NumericMetricMap = {};
 	for (const [key, entryValue] of Object.entries(metrics)) {
+		if (key === "__proto__" || key === "constructor" || key === "prototype") continue;
 		if (typeof entryValue === "number" && Number.isFinite(entryValue)) {
 			clone[key] = entryValue;
 		}
@@ -363,7 +366,12 @@ function hydrateMetricDefs(metricNames: string[] | undefined): MetricDef[] {
 
 function cloneAsi(value: unknown): ExperimentResult["asi"] {
 	if (typeof value !== "object" || value === null) return undefined;
-	return structuredClone(value) as ExperimentResult["asi"];
+	const clone: { [key: string]: unknown } = {};
+	for (const [key, entryValue] of Object.entries(value)) {
+		if (key === "__proto__" || key === "constructor" || key === "prototype") continue;
+		clone[key] = structuredClone(entryValue);
+	}
+	return clone as ExperimentResult["asi"];
 }
 
 function parseControlEntry(value: unknown): AutoresearchControlEntryData | null {
diff --git a/packages/coding-agent/src/autoresearch/tools/init-experiment.ts b/packages/coding-agent/src/autoresearch/tools/init-experiment.ts
index 5e81714ba..cf8a0f63f 100644
--- a/packages/coding-agent/src/autoresearch/tools/init-experiment.ts
+++ b/packages/coding-agent/src/autoresearch/tools/init-experiment.ts
@@ -17,6 +17,7 @@ import {
 	inferMetricUnitFromName,
 	isAutoresearchShCommand,
 	readMaxExperiments,
+	readPendingRunSummary,
 	resolveWorkDir,
 	validateWorkDir,
 } from "../helpers";
@@ -85,6 +86,19 @@ export function createInitExperimentTool(
 			const state = runtime.state;
 			const isReinitializing = state.results.length > 0;
 			const workDir = resolveWorkDir(ctx.cwd);
+			const pendingRun = await readPendingRunSummary(workDir, collectLoggedRunNumbers(state.results));
+			if (pendingRun) {
+				return {
+					content: [
+						{
+							type: "text",
+							text:
+								`Error: run #${pendingRun.runNumber} has not been logged yet. ` +
+								"Call log_experiment before re-initializing the current segment.",
+						},
+					],
+				};
+			}
 			const contractResult = readAutoresearchContract(workDir);
 			const scriptSnapshot = loadAutoresearchScriptSnapshot(workDir);
 			const errors = [...contractResult.errors, ...scriptSnapshot.errors];
@@ -241,6 +255,14 @@ export function createInitExperimentTool(
 			}
 
 			runtime.autoresearchMode = true;
+			runtime.autoResumeArmed = true;
+			runtime.lastAutoResumePendingRunNumber = null;
+			runtime.lastRunChecks = null;
+			runtime.lastRunDuration = null;
+			runtime.lastRunAsi = null;
+			runtime.lastRunArtifactDir = null;
+			runtime.lastRunNumber = null;
+			runtime.lastRunSummary = null;
 			options.dashboard.updateWidget(ctx, runtime);
 			options.dashboard.requestRender();
 
@@ -276,3 +298,13 @@ export function createInitExperimentTool(
 function renderInitCall(name: string, theme: Theme): string {
 	return `${theme.fg("toolTitle", theme.bold("init_experiment"))} ${theme.fg("accent", truncateToWidth(replaceTabs(name), 100))}`;
 }
+
+function collectLoggedRunNumbers(results: ExperimentState["results"]): Set<number> {
+	const runNumbers = new Set<number>();
+	for (const result of results) {
+		if (result.runNumber !== null) {
+			runNumbers.add(result.runNumber);
+		}
+	}
+	return runNumbers;
+}
diff --git a/packages/coding-agent/src/autoresearch/tools/log-experiment.ts b/packages/coding-agent/src/autoresearch/tools/log-experiment.ts
index 1a25db2ef..ec9f6caee 100644
--- a/packages/coding-agent/src/autoresearch/tools/log-experiment.ts
+++ b/packages/coding-agent/src/autoresearch/tools/log-experiment.ts
@@ -304,6 +304,8 @@ export function createLogExperimentTool(
 			runtime.lastRunArtifactDir = null;
 			runtime.lastRunNumber = null;
 			runtime.lastRunSummary = null;
+			runtime.autoResumeArmed = true;
+			runtime.lastAutoResumePendingRunNumber = null;
 
 			const currentSegmentRuns = currentResults(state.results, state.currentSegment).length;
 			const text = buildLogText(state, experiment, currentSegmentRuns, wallClockSeconds, gitNote);
@@ -364,10 +366,12 @@ function buildSecondaryMetrics(
 ): NumericMetricMap {
 	const merged: NumericMetricMap = {};
 	for (const [name, value] of Object.entries(parsedMetrics ?? {})) {
+		if (name === "__proto__" || name === "constructor" || name === "prototype") continue;
 		if (name === primaryMetricName) continue;
 		merged[name] = value;
 	}
 	for (const [name, value] of Object.entries(cloneMetrics(overrides))) {
+		if (name === "__proto__" || name === "constructor" || name === "prototype") continue;
 		merged[name] = value;
 	}
 	return merged;
@@ -377,6 +381,7 @@ function sanitizeAsi(value: { [key: string]: unknown } | undefined): ASIData | u
 	if (!value) return undefined;
 	const result: ASIData = {};
 	for (const [key, entryValue] of Object.entries(value)) {
+		if (key === "__proto__" || key === "constructor" || key === "prototype") continue;
 		const sanitized = sanitizeAsiValue(entryValue);
 		if (sanitized !== undefined) {
 			result[key] = sanitized;
@@ -398,6 +403,7 @@ function sanitizeAsiValue(value: unknown): ASIData[string] | undefined {
 		const objectValue = value as { [key: string]: unknown };
 		const result: ASIData = {};
 		for (const [key, entryValue] of Object.entries(objectValue)) {
+			if (key === "__proto__" || key === "constructor" || key === "prototype") continue;
 			const sanitized = sanitizeAsiValue(entryValue);
 			if (sanitized !== undefined) {
 				result[key] = sanitized;
@@ -567,6 +573,10 @@ async function revertFailedExperiment(
 		{ cwd: workDir, timeout: 10_000 },
 	);
 	const cleanResult = await options.pi.exec("git", ["clean", "-fd", "--", "."], { cwd: workDir, timeout: 10_000 });
+	const cleanIgnoredResult = await options.pi.exec("git", ["clean", "-fdX", "--", "."], {
+		cwd: workDir,
+		timeout: 10_000,
+	});
 	restoreAutoresearchFiles(preservedFiles);
 	if (restoreResult.code !== 0) {
 		return {
@@ -578,6 +588,11 @@ async function revertFailedExperiment(
 			error: `git clean failed: ${mergeStdoutStderr(cleanResult).trim() || `exit ${cleanResult.code}`}`,
 		};
 	}
+	if (cleanIgnoredResult.code !== 0) {
+		return {
+			error: `git clean -X failed: ${mergeStdoutStderr(cleanIgnoredResult).trim() || `exit ${cleanIgnoredResult.code}`}`,
+		};
+	}
 	const dirtyCheckResult = await options.pi.exec(
 		"git",
 		["status", "--porcelain=v1", "-z", "--untracked-files=all", "--", "."],
diff --git a/packages/coding-agent/src/autoresearch/tools/run-experiment.ts b/packages/coding-agent/src/autoresearch/tools/run-experiment.ts
index a393c3647..a6281a29f 100644
--- a/packages/coding-agent/src/autoresearch/tools/run-experiment.ts
+++ b/packages/coding-agent/src/autoresearch/tools/run-experiment.ts
@@ -303,6 +303,10 @@ export function createRunExperimentTool(
 				runDirectory,
 				runNumber,
 			};
+			runtime.autoResumeArmed = true;
+			runtime.lastAutoResumePendingRunNumber = null;
+			options.dashboard.updateWidget(ctx, runtime);
+			options.dashboard.requestRender();
 
 			await Bun.write(
 				runJsonPath,
diff --git a/packages/coding-agent/src/autoresearch/types.ts b/packages/coding-agent/src/autoresearch/types.ts
index 27ec82d02..e14fadac9 100644
--- a/packages/coding-agent/src/autoresearch/types.ts
+++ b/packages/coding-agent/src/autoresearch/types.ts
@@ -135,7 +135,9 @@ export interface RunningExperiment {
 
 export interface AutoresearchRuntime {
 	autoresearchMode: boolean;
+	autoResumeArmed: boolean;
 	dashboardExpanded: boolean;
+	lastAutoResumePendingRunNumber: number | null;
 	lastRunChecks: ChecksResult | null;
 	lastRunDuration: number | null;
 	lastRunAsi: ASIData | null;
diff --git a/packages/coding-agent/src/patch/hashline.ts b/packages/coding-agent/src/patch/hashline.ts
index 922eed2b6..58330de73 100644
--- a/packages/coding-agent/src/patch/hashline.ts
+++ b/packages/coding-agent/src/patch/hashline.ts
@@ -567,7 +567,7 @@ export function applyHashlineEdits(
 			const tag = formatLineTag(endLine + 1, nextSurvivingLine);
 			warnings.push(
 				`Possible boundary duplication: your last replacement line \`${trimmedLast}\` is identical to the next surviving line ${tag}. ` +
-				`If you meant to replace the entire block, set \`end\` to ${tag} instead.`,
+					`If you meant to replace the entire block, set \`end\` to ${tag} instead.`,
 			);
 		}
 	}
diff --git a/packages/coding-agent/src/prompts/tools/hashline.md b/packages/coding-agent/src/prompts/tools/hashline.md
index ff4f3702c..61749db87 100644
--- a/packages/coding-agent/src/prompts/tools/hashline.md
+++ b/packages/coding-agent/src/prompts/tools/hashline.md
@@ -114,4 +114,4 @@ When adding a sibling declaration, prefer `prepend` on the next declaration.
 - 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.
-</critical>
+</critical>
\ No newline at end of file
diff --git a/packages/coding-agent/test/agent-session-concurrent.test.ts b/packages/coding-agent/test/agent-session-concurrent.test.ts
index 42ccc162a..3c2011b06 100644
--- a/packages/coding-agent/test/agent-session-concurrent.test.ts
+++ b/packages/coding-agent/test/agent-session-concurrent.test.ts
@@ -6,8 +6,8 @@ import { afterEach, beforeEach, describe, expect, it, vi } from "bun:test";
 import * as fs from "node:fs";
 import * as os from "node:os";
 import * as path from "node:path";
-import { Agent, AgentBusyError, type AgentMessage, type AgentTool } from "@oh-my-pi/pi-agent-core";
-import { type AssistantMessage, getBundledModel, type ToolCall } from "@oh-my-pi/pi-ai";
+import { Agent, AgentBusyError, type AgentTool } from "@oh-my-pi/pi-agent-core";
+import { type AssistantMessage, getBundledModel, type Message, type ToolCall } from "@oh-my-pi/pi-ai";
 import { AssistantMessageEventStream } from "@oh-my-pi/pi-ai/utils/event-stream";
 import type { Rule } from "@oh-my-pi/pi-coding-agent/capability/rule";
 import { ModelRegistry } from "@oh-my-pi/pi-coding-agent/config/model-registry";
@@ -15,6 +15,7 @@ import { Settings } from "@oh-my-pi/pi-coding-agent/config/settings";
 import { TtsrManager } from "@oh-my-pi/pi-coding-agent/export/ttsr";
 import { AgentSession } from "@oh-my-pi/pi-coding-agent/session/agent-session";
 import { AuthStorage } from "@oh-my-pi/pi-coding-agent/session/auth-storage";
+import { convertToLlm } from "@oh-my-pi/pi-coding-agent/session/messages";
 import { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
 import { Snowflake } from "@oh-my-pi/pi-utils";
 import { Type } from "@sinclair/typebox";
@@ -112,6 +113,16 @@ describe("AgentSession concurrent prompt guard", () => {
 		return session;
 	}
 
+	async function waitFor(predicate: () => boolean, timeoutMs = 500): Promise<void> {
+		const deadline = Date.now() + timeoutMs;
+		while (Date.now() < deadline) {
+			if (predicate()) return;
+			await Bun.sleep(10);
+		}
+
+		throw new Error("Timed out waiting for condition");
+	}
+
 	it("should throw when prompt() called while streaming", async () => {
 		await createSession();
 
@@ -167,7 +178,7 @@ describe("AgentSession concurrent prompt guard", () => {
 	it("delivers hidden nextTurn stop reactions through the next LLM call without exposing them in the visible queue", async () => {
 		const model = getBundledModel("anthropic", "claude-sonnet-4-5")!;
 		let firstStream: MockAssistantStream | undefined;
-		const callMessages: AgentMessage[][] = [];
+		const callMessages: Message[][] = [];
 
 		const agent = new Agent({
 			getApiKey: () => "test-key",
@@ -176,6 +187,7 @@ describe("AgentSession concurrent prompt guard", () => {
 				systemPrompt: "Test",
 				tools: [],
 			},
+			convertToLlm,
 			streamFn: (_model, context) => {
 				callMessages.push([...context.messages]);
 				const stream = new MockAssistantStream();
@@ -206,7 +218,7 @@ describe("AgentSession concurrent prompt guard", () => {
 		});
 
 		const firstPrompt = session.prompt("First message");
-		await Bun.sleep(10);
+		await waitFor(() => session.isStreaming && firstStream !== undefined && callMessages.length === 1);
 
 		await session.sendCustomMessage(
 			{
@@ -227,10 +239,15 @@ describe("AgentSession concurrent prompt guard", () => {
 
 		expect(callMessages).toHaveLength(2);
 		expect(
-			callMessages[1]?.some(
-				message =>
-					message.role === "custom" && "customType" in message && message.customType === "autoresearch-resume",
-			),
+			callMessages[1]?.some(message => {
+				if (typeof message.content === "string") {
+					return message.content.includes("Hidden stop reaction");
+				}
+
+				return message.content.some(
+					content => content.type === "text" && content.text.includes("Hidden stop reaction"),
+				);
+			}),
 		).toBe(true);
 	});
 
diff --git a/packages/coding-agent/test/autoresearch-state.test.ts b/packages/coding-agent/test/autoresearch-state.test.ts
index a5d20eb17..db59e877a 100644
--- a/packages/coding-agent/test/autoresearch-state.test.ts
+++ b/packages/coding-agent/test/autoresearch-state.test.ts
@@ -297,6 +297,12 @@ describe("autoresearch command guard", () => {
 		expect(isAutoresearchShCommand("echo hi; autoresearch.sh")).toBe(false);
 		expect(isAutoresearchShCommand("bash -lc 'autoresearch.sh'")).toBe(false);
 	});
+
+	it("rejects chained or redirected benchmark commands even when autoresearch.sh comes first", () => {
+		expect(isAutoresearchShCommand("bash autoresearch.sh && touch /tmp/marker")).toBe(false);
+		expect(isAutoresearchShCommand("./autoresearch.sh | tee run.log")).toBe(false);
+		expect(isAutoresearchShCommand("./autoresearch.sh > run.log")).toBe(false);
+	});
 });
 
 interface AutoresearchCommandHarness {
@@ -394,6 +400,9 @@ function createAutoresearchCommandHarness(
 }
 
 interface AutoresearchLifecycleHarness {
+	beforeAgentStartHandler:
+		| ((event: { systemPrompt: string }, ctx: ExtensionContext) => Promise<unknown> | unknown)
+		| undefined;
 	sessionStartHandler: ((event: SessionStartEvent, ctx: ExtensionContext) => Promise<void> | void) | undefined;
 	sessionSwitchHandler: ((event: SessionSwitchEvent, ctx: ExtensionContext) => Promise<void> | void) | undefined;
 	agentEndHandler: ((event: unknown, ctx: ExtensionContext) => Promise<void> | void) | undefined;
@@ -475,6 +484,9 @@ function createAutoresearchLifecycleHarness(options: {
 	} as unknown as ExtensionContext;
 
 	return {
+		beforeAgentStartHandler: handlers.get("before_agent_start") as
+			| ((event: { systemPrompt: string }, ctx: ExtensionContext) => Promise<unknown> | unknown)
+			| undefined,
 		sessionStartHandler: handlers.get("session_start") as
 			| ((event: SessionStartEvent, ctx: ExtensionContext) => Promise<void> | void)
 			| undefined,
@@ -515,6 +527,7 @@ describe("autoresearch command startup", () => {
 				"runtime_ms",
 				"ms",
 				"lower",
+				"memory_mb, rss_mb",
 				"packages/coding-agent/src/autoresearch, packages/coding-agent/test",
 				"packages/coding-agent/src/generated",
 				"preserve output format",
@@ -547,6 +560,7 @@ describe("autoresearch command startup", () => {
 			{ title: "Primary Metric Name", placeholder: "runtime_ms" },
 			{ title: "Metric Unit", placeholder: "ms" },
 			{ title: "Metric Direction", placeholder: "lower" },
+			{ title: "Tradeoff Metrics", placeholder: "" },
 			{ title: "Files in Scope", placeholder: "packages/coding-agent/src/autoresearch" },
 			{ title: "Off Limits", placeholder: "" },
 			{ title: "Constraints", placeholder: "" },
@@ -558,6 +572,8 @@ describe("autoresearch command startup", () => {
 		expect(harness.sentMessages[0]).toContain("primary metric: `runtime_ms`");
 		expect(harness.sentMessages[0]).toContain("metric unit: `ms`");
 		expect(harness.sentMessages[0]).toContain("direction: `lower`");
+		expect(harness.sentMessages[0]).toContain("`memory_mb`");
+		expect(harness.sentMessages[0]).toContain("`rss_mb`");
 		expect(harness.sentMessages[0]).toContain("`packages/coding-agent/src/autoresearch`");
 		expect(harness.sentMessages[0]).toContain("`packages/coding-agent/src/generated`");
 		expect(harness.sentMessages[0]).toContain("preserve output format");
@@ -587,21 +603,17 @@ describe("autoresearch command startup", () => {
 		await harness.command.handler("", harness.ctx);
 
 		expect(harness.inputCalls).toEqual([]);
-		expect(harness.sentMessages).toEqual([
-			[
-				"Resume autoresearch from the attached notes.",
-				"",
-				`@${autoresearchMdPath}`,
-				"",
-				"Using dedicated git branch `autoresearch/existing-20260322`.",
-				"",
-				"Use the notes as the source of truth for the current direction, scope, and constraints.",
-				"- inspect recent git history for context",
-				"- inspect `autoresearch.jsonl` if it exists",
-				"- continue the most promising unfinished branch",
-				"- keep iterating until interrupted or until the configured iteration cap is reached",
-			].join("\n"),
-		]);
+		expect(harness.sentMessages).toHaveLength(1);
+		expect(harness.sentMessages[0]).toContain("Resume autoresearch from the attached notes.");
+		expect(harness.sentMessages[0]).toContain(`@${autoresearchMdPath}`);
+		expect(harness.sentMessages[0]).toContain("Using dedicated git branch `autoresearch/existing-20260322`.");
+		expect(harness.sentMessages[0]).toContain(
+			"Use the notes as the source of truth for the current direction, scope, and constraints.",
+		);
+		expect(harness.sentMessages[0]).toContain("- inspect `autoresearch.jsonl` if it exists");
+		expect(harness.sentMessages[0]).toContain(
+			"- continue the most promising unfinished direction on the current protected branch",
+		);
 	});
 
 	it("includes explicit resume context when the user resumes with additional instructions", async () => {
@@ -642,6 +654,7 @@ describe("autoresearch command startup", () => {
 				"runtime_ms",
 				"ms",
 				"lower",
+				"",
 				"packages/coding-agent/src/autoresearch",
 				"",
 				"",
@@ -741,12 +754,16 @@ describe("autoresearch command startup", () => {
 				"runtime_ms",
 				"ms",
 				"lower",
+				"",
 				"packages/coding-agent/src/autoresearch",
 				"",
 				"",
 			],
 			async (command, args) => {
 				if (command !== "git") return { code: 1, stderr: "unexpected command", stdout: "" };
+				if (args[0] === "rev-parse" && args[1] === "--show-prefix") {
+					return { code: 0, stderr: "", stdout: "" };
+				}
 				if (args[0] === "rev-parse") return { code: 0, stderr: "", stdout: `${dir}\n` };
 				if (args[0] === "branch" && args[1] === "--show-current") {
 					return { code: 0, stderr: "", stdout: "main\n" };
@@ -782,12 +799,16 @@ describe("autoresearch command startup", () => {
 				"runtime_ms",
 				"ms",
 				"lower",
+				"",
 				"packages/coding-agent/src/autoresearch",
 				"",
 				"",
 			],
 			async (command, args) => {
 				if (command !== "git") return { code: 1, stderr: "unexpected command", stdout: "" };
+				if (args[0] === "rev-parse" && args[1] === "--show-prefix") {
+					return { code: 0, stderr: "", stdout: "" };
+				}
 				if (args[0] === "rev-parse") return { code: 0, stderr: "", stdout: `${dir}\n` };
 				if (args[0] === "branch" && args[1] === "--show-current") {
 					return { code: 0, stderr: "", stdout: "main\n" };
@@ -814,6 +835,7 @@ describe("autoresearch command startup", () => {
 				"runtime_ms",
 				"ms",
 				"lower",
+				"",
 				"packages/coding-agent/src/autoresearch",
 				"",
 				"",
@@ -1057,6 +1079,99 @@ describe("autoresearch auto-resume", () => {
 			triggerTurn: true,
 		});
 	});
+
+	it("does not enqueue another hidden turn after a passive autoresearch turn with no pending run", async () => {
+		const dir = makeTempDir();
+		tempDirs.push(dir);
+		fs.writeFileSync(
+			path.join(dir, "autoresearch.jsonl"),
+			`${JSON.stringify({ type: "config", metricName: "runtime_ms", scopePaths: ["src"] })}\n`,
+		);
+
+		const harness = createAutoresearchLifecycleHarness({
+			activeTools: ["init_experiment", "run_experiment", "log_experiment"],
+			controlEntries: [{ type: "custom", customType: "autoresearch-control", data: { mode: "on", goal: "x" } }],
+			cwd: dir,
+		});
+
+		await harness.sessionStartHandler?.({ type: "session_start" } as SessionStartEvent, harness.ctx);
+		await harness.agentEndHandler?.({}, harness.ctx);
+
+		expect(harness.sentMessages).toEqual([]);
+	});
+
+	it("renders the high-signal prompt sections for playbooks, backlog, recent runs, and pending runs", async () => {
+		const dir = makeTempDir();
+		tempDirs.push(dir);
+		fs.writeFileSync(path.join(dir, "autoresearch.md"), "# Autoresearch\n");
+		fs.writeFileSync(path.join(dir, "autoresearch.program.md"), "# Local Playbook\n");
+		fs.writeFileSync(path.join(dir, "autoresearch.ideas.md"), "- try batching\n");
+		fs.writeFileSync(path.join(dir, "autoresearch.checks.sh"), "#!/usr/bin/env bash\n");
+		fs.writeFileSync(
+			path.join(dir, "autoresearch.jsonl"),
+			[
+				JSON.stringify({
+					type: "config",
+					metricName: "runtime_ms",
+					metricUnit: "ms",
+					scopePaths: ["src"],
+				}),
+				JSON.stringify({
+					run: 1,
+					commit: "aaaaaaa",
+					metric: 10,
+					status: "keep",
+					description: "baseline",
+					timestamp: 1,
+					asi: { hypothesis: "baseline" },
+				}),
+				JSON.stringify({
+					run: 2,
+					commit: "bbbbbbb",
+					metric: 9,
+					status: "discard",
+					description: "too noisy",
+					timestamp: 2,
+					asi: {
+						hypothesis: "raise cache size",
+						rollback_reason: "noise",
+						next_action_hint: "re-test with more samples",
+					},
+				}),
+			].join("\n"),
+		);
+		await Bun.write(
+			path.join(dir, ".autoresearch", "runs", "0003", "run.json"),
+			JSON.stringify({
+				command: "bash autoresearch.sh",
+				completedAt: new Date().toISOString(),
+				durationSeconds: 1,
+				exitCode: 0,
+				parsedPrimary: 8,
+				runNumber: 3,
+			}),
+		);
+
+		const harness = createAutoresearchLifecycleHarness({
+			activeTools: ["init_experiment", "run_experiment", "log_experiment"],
+			controlEntries: [{ type: "custom", customType: "autoresearch-control", data: { mode: "on", goal: "x" } }],
+			cwd: dir,
+		});
+
+		await harness.sessionStartHandler?.({ type: "session_start" } as SessionStartEvent, harness.ctx);
+		const result = await harness.beforeAgentStartHandler?.({ systemPrompt: "BASE" }, harness.ctx);
+		const systemPrompt =
+			typeof result === "object" && result !== null && "systemPrompt" in result
+				? String((result as { systemPrompt: string }).systemPrompt)
+				: "";
+
+		expect(systemPrompt).toContain("### Local Playbook");
+		expect(systemPrompt).toContain("### Current Segment Snapshot");
+		expect(systemPrompt).toContain("### Pending Run");
+		expect(systemPrompt).toContain("### Ideas backlog");
+		expect(systemPrompt).toContain("Recent runs:");
+		expect(systemPrompt).toContain("finish the `log_experiment` step before starting another benchmark");
+	});
 });
 
 describe("autoresearch lifecycle tool activation", () => {
diff --git a/packages/coding-agent/test/autoresearch-tools.test.ts b/packages/coding-agent/test/autoresearch-tools.test.ts
index 068c16452..19ae7f6f1 100644
--- a/packages/coding-agent/test/autoresearch-tools.test.ts
+++ b/packages/coding-agent/test/autoresearch-tools.test.ts
@@ -245,6 +245,24 @@ describe("autoresearch tools", () => {
 		});
 
 		const runtime = createSessionRuntime();
+		runtime.lastRunChecks = { pass: true, output: "stale", duration: 1 };
+		runtime.lastRunDuration = 1;
+		runtime.lastRunAsi = { hypothesis: "stale" };
+		runtime.lastRunArtifactDir = path.join(dir, ".autoresearch", "runs", "9999");
+		runtime.lastRunNumber = 99;
+		runtime.lastRunSummary = {
+			checksDurationSeconds: 1,
+			checksPass: true,
+			checksTimedOut: false,
+			command: "bash autoresearch.sh",
+			durationSeconds: 1,
+			parsedAsi: { hypothesis: "stale" },
+			parsedMetrics: { runtime_ms: 10 },
+			parsedPrimary: 10,
+			passed: true,
+			runDirectory: path.join(dir, ".autoresearch", "runs", "9999"),
+			runNumber: 99,
+		};
 		const tool = createInitExperimentTool({
 			dashboard: createDashboardStub(),
 			getRuntime: () => runtime,
@@ -291,6 +309,12 @@ describe("autoresearch tools", () => {
 		expect(configEntry.offLimits).toEqual(["src/generated"]);
 		expect(configEntry.constraints).toEqual(["keep behavior stable"]);
 		expect(configEntry.segmentFingerprint).toBe(createFingerprint(dir));
+		expect(runtime.lastRunChecks).toBeNull();
+		expect(runtime.lastRunDuration).toBeNull();
+		expect(runtime.lastRunAsi).toBeNull();
+		expect(runtime.lastRunArtifactDir).toBeNull();
+		expect(runtime.lastRunNumber).toBeNull();
+		expect(runtime.lastRunSummary).toBeNull();
 	});
 
 	it("rejects init_experiment when the passed contract no longer matches autoresearch.md", async () => {
@@ -349,6 +373,53 @@ describe("autoresearch tools", () => {
 		expect(fs.existsSync(path.join(dir, "autoresearch.jsonl"))).toBe(false);
 	});
 
+	it("rejects init_experiment while a previous run is still pending", async () => {
+		const dir = makeTempDir();
+		tempDirs.push(dir);
+		writeAutoresearchWorkspace(dir);
+		await Bun.write(
+			path.join(dir, ".autoresearch", "runs", "0001", "run.json"),
+			JSON.stringify({
+				command: "bash autoresearch.sh",
+				completedAt: new Date().toISOString(),
+				durationSeconds: 1,
+				exitCode: 0,
+				parsedPrimary: 10,
+				runNumber: 1,
+			}),
+		);
+
+		const runtime = createSessionRuntime();
+		const tool = createInitExperimentTool({
+			dashboard: createDashboardStub(),
+			getRuntime: () => runtime,
+			pi: {} as ExtensionAPI,
+		});
+
+		const result = await tool.execute(
+			"init-pending",
+			{
+				name: "Blocked",
+				metric_name: "runtime_ms",
+				metric_unit: "ms",
+				direction: "lower",
+				benchmark_command: "bash autoresearch.sh",
+				scope_paths: ["src"],
+				off_limits: [],
+				constraints: [],
+			},
+			undefined,
+			undefined,
+			createContext(dir),
+		);
+
+		expect(result.content[0]).toEqual({
+			type: "text",
+			text: expect.stringContaining("has not been logged yet"),
+		});
+		expect(fs.existsSync(path.join(dir, "autoresearch.jsonl"))).toBe(false);
+	});
+
 	it("refuses to start a new benchmark while a previous run artifact is still unlogged", async () => {
 		const dir = makeTempDir();
 		tempDirs.push(dir);
@@ -512,6 +583,8 @@ describe("autoresearch tools", () => {
 		await $`git config user.name Test User`.cwd(dir).quiet();
 		await $`git add .`.cwd(dir).quiet();
 		await $`git commit -m initial`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-force-secondary-accept`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-keep`.cwd(dir).quiet();
 
 		fs.writeFileSync(path.join(dir, "src", "in-scope.ts"), "export const value = 3;\n");
 		fs.writeFileSync(path.join(dir, "autoresearch.program.md"), "# Strategy\n\n- focus on in-scope edits\n");
@@ -618,6 +691,8 @@ describe("autoresearch tools", () => {
 		await $`git config user.name Test User`.cwd(dir).quiet();
 		await $`git add .`.cwd(dir).quiet();
 		await $`git commit -m initial`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-max-iterations-accept`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-force-secondary`.cwd(dir).quiet();
 
 		fs.writeFileSync(path.join(dir, "src", "out-of-scope.ts"), "export const value = 99;\n");
 		await Bun.write(
@@ -707,6 +782,8 @@ describe("autoresearch tools", () => {
 		await $`git config user.name Test User`.cwd(dir).quiet();
 		await $`git add .`.cwd(dir).quiet();
 		await $`git commit -m initial`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-discard-cleanup`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-max-iterations`.cwd(dir).quiet();
 
 		fs.writeFileSync(path.join(dir, "src", "generated", "index.ts"), "export const value = 2;\n");
 		await Bun.write(
@@ -776,6 +853,7 @@ describe("autoresearch tools", () => {
 		await $`git config user.name Test User`.cwd(dir).quiet();
 		await $`git add .`.cwd(dir).quiet();
 		await $`git commit -m initial`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-discard`.cwd(dir).quiet();
 
 		await Bun.write(
 			path.join(dir, ".autoresearch", "runs", "0003", "run.json"),
@@ -861,6 +939,280 @@ describe("autoresearch tools", () => {
 		expect(runtime.state.results).toHaveLength(2);
 	});
 
+	it("rejects log_experiment when configured secondary metrics are missing", async () => {
+		const dir = makeTempDir();
+		tempDirs.push(dir);
+		writeAutoresearchWorkspace(dir);
+		await Bun.write(
+			path.join(dir, ".autoresearch", "runs", "0001", "run.json"),
+			JSON.stringify({
+				command: "bash autoresearch.sh",
+				completedAt: new Date().toISOString(),
+				durationSeconds: 1,
+				exitCode: 0,
+				parsedMetrics: { memory_mb: 32, runtime_ms: 9 },
+				parsedPrimary: 9,
+				runNumber: 1,
+			}),
+		);
+
+		const runtime = createSessionRuntime();
+		runtime.state.metricName = "runtime_ms";
+		runtime.state.metricUnit = "ms";
+		runtime.state.secondaryMetrics = [
+			{ name: "memory_mb", unit: "mb" },
+			{ name: "tokens", unit: "" },
+		];
+		runtime.state.segmentFingerprint = createFingerprint(dir);
+		runtime.lastRunSummary = {
+			checksDurationSeconds: 0,
+			checksPass: null,
+			checksTimedOut: false,
+			command: "bash autoresearch.sh",
+			durationSeconds: 1,
+			parsedAsi: null,
+			parsedMetrics: { memory_mb: 32, runtime_ms: 9 },
+			parsedPrimary: 9,
+			passed: true,
+			runDirectory: path.join(dir, ".autoresearch", "runs", "0001"),
+			runNumber: 1,
+		};
+
+		const tool = createLogExperimentTool({
+			dashboard: createDashboardStub(),
+			getRuntime: () => runtime,
+			pi: {} as ExtensionAPI,
+		});
+		const result = await tool.execute(
+			"call-missing-secondary",
+			{
+				commit: "initial",
+				metric: 9,
+				status: "discard",
+				description: "missing tokens metric",
+				metrics: { memory_mb: 32 },
+				asi: {
+					hypothesis: "watch memory only",
+					rollback_reason: "missing required metrics",
+					next_action_hint: "include all configured tradeoff metrics",
+				},
+			},
+			undefined,
+			undefined,
+			createContext(dir),
+		);
+
+		expect(result.content[0]).toEqual({
+			type: "text",
+			text: expect.stringContaining("missing secondary metrics: tokens"),
+		});
+		expect(runtime.state.results).toHaveLength(0);
+	});
+
+	it("rejects new secondary metrics unless force is enabled", async () => {
+		const dir = makeTempDir();
+		tempDirs.push(dir);
+		writeAutoresearchWorkspace(dir);
+		await Bun.write(
+			path.join(dir, ".autoresearch", "runs", "0001", "run.json"),
+			JSON.stringify({
+				command: "bash autoresearch.sh",
+				completedAt: new Date().toISOString(),
+				durationSeconds: 1,
+				exitCode: 0,
+				parsedMetrics: { runtime_ms: 9 },
+				parsedPrimary: 9,
+				runNumber: 1,
+			}),
+		);
+
+		const runtime = createSessionRuntime();
+		runtime.state.metricName = "runtime_ms";
+		runtime.state.metricUnit = "ms";
+		runtime.state.secondaryMetrics = [{ name: "memory_mb", unit: "mb" }];
+		runtime.state.segmentFingerprint = createFingerprint(dir);
+		runtime.lastRunSummary = {
+			checksDurationSeconds: 0,
+			checksPass: null,
+			checksTimedOut: false,
+			command: "bash autoresearch.sh",
+			durationSeconds: 1,
+			parsedAsi: null,
+			parsedMetrics: { runtime_ms: 9 },
+			parsedPrimary: 9,
+			passed: true,
+			runDirectory: path.join(dir, ".autoresearch", "runs", "0001"),
+			runNumber: 1,
+		};
+
+		const tool = createLogExperimentTool({
+			dashboard: createDashboardStub(),
+			getRuntime: () => runtime,
+			pi: {} as ExtensionAPI,
+		});
+		const result = await tool.execute(
+			"call-new-secondary",
+			{
+				commit: "initial",
+				metric: 9,
+				status: "discard",
+				description: "introduce tokens metric",
+				metrics: { memory_mb: 32, tokens: 100 },
+				asi: {
+					hypothesis: "watch an extra tradeoff",
+					rollback_reason: "needs explicit opt-in",
+					next_action_hint: "retry with force if the metric matters",
+				},
+			},
+			undefined,
+			undefined,
+			createContext(dir),
+		);
+
+		expect(result.content[0]).toEqual({
+			type: "text",
+			text: expect.stringContaining("new secondary metrics require force=true: tokens"),
+		});
+		expect(runtime.state.results).toHaveLength(0);
+	});
+
+	it("accepts a new secondary metric when force is enabled", async () => {
+		const dir = makeTempDir();
+		tempDirs.push(dir);
+		writeAutoresearchWorkspace(dir);
+
+		await $`git init`.cwd(dir).quiet();
+		await $`git config user.email test@example.com`.cwd(dir).quiet();
+		await $`git config user.name Test User`.cwd(dir).quiet();
+		await $`git add .`.cwd(dir).quiet();
+		await $`git commit -m initial`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-force-secondary-accept`.cwd(dir).quiet();
+
+		await Bun.write(
+			path.join(dir, ".autoresearch", "runs", "0001", "run.json"),
+			JSON.stringify({
+				command: "bash autoresearch.sh",
+				completedAt: new Date().toISOString(),
+				durationSeconds: 1,
+				exitCode: 0,
+				parsedMetrics: { runtime_ms: 9 },
+				parsedPrimary: 9,
+				runNumber: 1,
+			}),
+		);
+
+		const runtime = createSessionRuntime();
+		runtime.state.metricName = "runtime_ms";
+		runtime.state.metricUnit = "ms";
+		runtime.state.secondaryMetrics = [{ name: "memory_mb", unit: "mb" }];
+		runtime.state.segmentFingerprint = createFingerprint(dir);
+		runtime.lastRunSummary = {
+			checksDurationSeconds: 0,
+			checksPass: null,
+			checksTimedOut: false,
+			command: "bash autoresearch.sh",
+			durationSeconds: 1,
+			parsedAsi: null,
+			parsedMetrics: { runtime_ms: 9 },
+			parsedPrimary: 9,
+			passed: true,
+			runDirectory: path.join(dir, ".autoresearch", "runs", "0001"),
+			runNumber: 1,
+		};
+
+		const tool = createLogExperimentTool({
+			dashboard: createDashboardStub(),
+			getRuntime: () => runtime,
+			pi: createGitApi(),
+		});
+		const result = await tool.execute(
+			"call-force-secondary",
+			{
+				commit: "initial",
+				metric: 9,
+				status: "discard",
+				description: "force extra metric",
+				force: true,
+				metrics: { memory_mb: 32, tokens: 100 },
+				asi: {
+					hypothesis: "capture an extra tradeoff",
+					rollback_reason: "benchmark was flat",
+					next_action_hint: "keep collecting tokens when useful",
+				},
+			},
+			undefined,
+			undefined,
+			createContext(dir),
+		);
+
+		expect(result.content[0]).toEqual({
+			type: "text",
+			text: expect.stringContaining("Logged run #1: discard"),
+		});
+		expect(runtime.state.secondaryMetrics).toContainEqual({ name: "tokens", unit: "" });
+	});
+
+	it("rejects log_experiment at the tool boundary when asi is missing", async () => {
+		const dir = makeTempDir();
+		tempDirs.push(dir);
+		writeAutoresearchWorkspace(dir);
+		await Bun.write(
+			path.join(dir, ".autoresearch", "runs", "0001", "run.json"),
+			JSON.stringify({
+				command: "bash autoresearch.sh",
+				completedAt: new Date().toISOString(),
+				durationSeconds: 1,
+				exitCode: 0,
+				parsedMetrics: { runtime_ms: 9 },
+				parsedPrimary: 9,
+				runNumber: 1,
+			}),
+		);
+
+		const runtime = createSessionRuntime();
+		runtime.state.metricName = "runtime_ms";
+		runtime.state.metricUnit = "ms";
+		runtime.state.segmentFingerprint = createFingerprint(dir);
+		runtime.lastRunSummary = {
+			checksDurationSeconds: 0,
+			checksPass: null,
+			checksTimedOut: false,
+			command: "bash autoresearch.sh",
+			durationSeconds: 1,
+			parsedAsi: null,
+			parsedMetrics: { runtime_ms: 9 },
+			parsedPrimary: 9,
+			passed: true,
+			runDirectory: path.join(dir, ".autoresearch", "runs", "0001"),
+			runNumber: 1,
+		};
+
+		const tool = createLogExperimentTool({
+			dashboard: createDashboardStub(),
+			getRuntime: () => runtime,
+			pi: {} as ExtensionAPI,
+		});
+		const result = await tool.execute(
+			"call-missing-asi",
+			{
+				commit: "initial",
+				metric: 9,
+				status: "keep",
+				description: "missing asi",
+			},
+			undefined,
+			undefined,
+			createContext(dir),
+		);
+
+		expect(result.content[0]).toEqual({
+			type: "text",
+			text: expect.stringContaining("asi is required"),
+		});
+		expect(runtime.state.results).toHaveLength(0);
+		expect(fs.existsSync(path.join(dir, "autoresearch.jsonl"))).toBe(false);
+	});
+
 	it("requires failed benchmarks to be logged as crash", async () => {
 		const dir = makeTempDir();
 		tempDirs.push(dir);
@@ -1002,6 +1354,7 @@ describe("autoresearch tools", () => {
 		await $`git config user.name Test User`.cwd(dir).quiet();
 		await $`git add .`.cwd(dir).quiet();
 		await $`git commit -m initial`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-max-iterations-accept`.cwd(dir).quiet();
 
 		await Bun.write(
 			path.join(dir, ".autoresearch", "runs", "0001", "run.json"),
@@ -1164,6 +1517,7 @@ describe("autoresearch tools", () => {
 		await $`git config user.name Test User`.cwd(dir).quiet();
 		await $`git add .`.cwd(dir).quiet();
 		await $`git commit -m initial`.cwd(dir).quiet();
+		await $`git checkout -b autoresearch/test-discard-cleanup`.cwd(dir).quiet();
 
 		fs.mkdirSync(path.join(dir, "tmp-artifact"), { recursive: true });
 		fs.writeFileSync(path.join(dir, "tmp-artifact", "result.txt"), "temporary benchmark output\n");
diff --git a/packages/coding-agent/test/core/hashline.test.ts b/packages/coding-agent/test/core/hashline.test.ts
index d1edbccd3..311ed743d 100644
--- a/packages/coding-agent/test/core/hashline.test.ts
+++ b/packages/coding-agent/test/core/hashline.test.ts
@@ -535,7 +535,9 @@ describe("applyHashlineEdits — heuristics", () => {
 		];
 		const result = applyHashlineEdits(content, edits);
 		expect(result.lines).toBe("if (ok) {\n  runSafe();\n}\n}\nafter();");
-		expect(result.warnings).toBeUndefined();
+		expect(result.warnings).toHaveLength(1);
+		expect(result.warnings?.[0]).toContain("Possible boundary duplication");
+		expect(result.warnings?.[0]).toContain("set `end` to 3#RZ");
 	});
 
 	it("preserves duplicated trailing content when replacement re-emits the next line", () => {
@@ -550,7 +552,9 @@ describe("applyHashlineEdits — heuristics", () => {
 		];
 		const result = applyHashlineEdits(content, edits);
 		expect(result.lines).toBe("start\n  newCall();\nnextCall();\nnextCall();\nafter();");
-		expect(result.warnings).toBeUndefined();
+		expect(result.warnings).toHaveLength(1);
+		expect(result.warnings?.[0]).toContain("Possible boundary duplication");
+		expect(result.warnings?.[0]).toContain("set `end` to 3#HR");
 	});
 
 	it("preserves duplicated leading content when replacement re-emits the previous line", () => {