@scanton/phase2s 1.0.0 → 1.8.0

package/dist/src/cli/goal.js

@@ -6,37 +6,100 @@
  * output, retries failed sub-tasks with failure context, and loops until all
  * criteria pass or max attempts are exhausted.
  *
- * Usage: phase2s goal <spec-file> [--max-attempts <n>]
+ * Usage: phase2s goal <spec-file> [--max-attempts <n>] [--resume] [--review-before-run]
+ *
+ * With --resume: reads existing state from .phase2s/state/<hash>.json
+ * (relative to the spec file directory), skips completed sub-tasks, and
+ * injects saved failure context for failed ones. Starts fresh if no state
+ * exists.
+ *
+ * With --review-before-run: runs the spec through adversarial review (fresh
+ * Agent instance, adversarial SKILL.md template) before execution begins.
+ * Halts and returns challenged: true if verdict is CHALLENGED or
+ * NEEDS_CLARIFICATION.
  */
 import { execFile } from "child_process";
 import { readFileSync } from "fs";
-import { resolve } from "path";
+import { resolve, dirname, basename } from "path";
 import { Agent } from "../core/agent.js";
 import { loadConfig } from "../core/config.js";
 import { loadLearnings, formatLearningsForPrompt } from "../core/memory.js";
 import { parseSpec } from "../core/spec-parser.js";
+import { computeSpecHash, readState, writeState, clearState } from "../core/state.js";
+import { RunLogger } from "../core/run-logger.js";
+import { sendNotification, buildNotifyPayload } from "../core/notify.js";
 import { loadAllSkills } from "../skills/index.js";
 import { substituteInputs, stripAskTokens } from "../skills/template.js";
+/** Cap on bytes stored for failureContext per sub-task. */
+const FAILURE_CONTEXT_MAX_BYTES = 4096;
 export async function runGoal(specFile, options = {}) {
     const specPath = resolve(process.cwd(), specFile);
+    // State and run logs are stored relative to the spec file directory, not
+    // invocation cwd. This keeps logs next to the spec regardless of where
+    // `phase2s goal` is invoked from.
+    const specDir = dirname(specPath);
     let markdown;
     try {
         markdown = readFileSync(specPath, "utf8");
     }
     catch {
-        console.error(`Error: Cannot read spec file: ${specPath}`);
-        process.exit(1);
+        throw new Error(`Cannot read spec file: ${specPath}`);
     }
+    const specHash = computeSpecHash(markdown);
     const spec = parseSpec(markdown);
     const maxAttempts = Math.max(1, parseInt(options.maxAttempts ?? "3", 10) || 3);
+    const resume = !!options.resume;
+    // Initialise RunLogger now so we can capture the path even if we halt early.
+    const logger = new RunLogger(specDir, specHash);
+    const startMs = Date.now();
+    // Load config early so it's available for all return paths (including early exits).
+    const config = await loadConfig();
+    // -------------------------------------------------------------------------
+    // State: load existing state when resuming, otherwise start fresh.
+    // -------------------------------------------------------------------------
+    let state = resume ? readState(specDir, specHash) : null;
+    // If --resume but no prior state found: silently start fresh (no error).
+    if (state === null) {
+        state = {
+            specFile: basename(specPath),
+            specHash,
+            startedAt: new Date().toISOString(),
+            lastUpdatedAt: new Date().toISOString(),
+            maxAttempts,
+            attempt: 0,
+            subTaskResults: {},
+        };
+    }
+    logger.log({
+        event: "goal_started",
+        specFile: basename(specPath),
+        specHash,
+        subTaskCount: spec.decomposition.length,
+        maxAttempts,
+        resuming: resume,
+    });
     console.log(`\nGoal executor: ${spec.title}`);
     console.log(`Eval command: ${spec.evalCommand}`);
     console.log(`Sub-tasks: ${spec.decomposition.length}`);
     console.log(`Acceptance criteria: ${spec.acceptanceCriteria.length}`);
     console.log(`Max attempts: ${maxAttempts}`);
+    if (resume) {
+        const doneCount = Object.values(state.subTaskResults).filter((r) => r.status === "passed").length;
+        console.log(`Resuming: ${doneCount}/${spec.decomposition.length} sub-tasks already completed`);
+    }
     if (spec.decomposition.length === 0 && spec.acceptanceCriteria.length === 0) {
         console.log("\nSpec has no sub-tasks and no acceptance criteria. Nothing to execute.");
-        return { success: true, attempts: 0, criteriaResults: {} };
+        logger.log({ event: "goal_completed", success: true, attempts: 0 });
+        const result = {
+            success: true,
+            attempts: 0,
+            criteriaResults: {},
+            runLogPath: logger.close(),
+            summary: "Spec has no sub-tasks and no acceptance criteria.",
+            durationMs: Date.now() - startMs,
+        };
+        await maybeNotify(options, config, result, basename(specPath));
+        return result;
     }
     // Warn on large specs
     if (spec.decomposition.length * maxAttempts > 15) {
@@ -44,74 +107,262 @@ export async function runGoal(specFile, options = {}) {
             "This may take a while and consume significant ChatGPT usage.");
     }
     // Set up agent
-    const config = await loadConfig();
     const learningsList = await loadLearnings(process.cwd());
     const learningsStr = formatLearningsForPrompt(learningsList);
-    const agent = new Agent({ config, learnings: learningsStr });
-    // Load skills to get satori template + settings
+    // Load skills to get satori + adversarial templates and settings
     const skills = await loadAllSkills();
     const satoriSkill = skills.find((s) => s.name === "satori");
+    const adversarialSkill = skills.find((s) => s.name === "adversarial");
     const satoriRetries = satoriSkill?.retries ?? 3;
     const satoriModel = satoriSkill?.model;
+    const adversarialModel = adversarialSkill?.model;
     // Build the satori base prompt from its template (same as what the REPL does)
     const satoriTemplate = satoriSkill
         ? stripAskTokens(substituteInputs(satoriSkill.promptTemplate, {}, satoriSkill.inputs)).result
         : "";
-    let attempt = 0;
+    // -------------------------------------------------------------------------
+    // Pre-execution adversarial review (optional, uses fresh Agent to avoid
+    // contaminating the implementation agent's conversation history).
+    // -------------------------------------------------------------------------
+    if (options.reviewBeforeRun) {
+        logger.log({ event: "plan_review_started" });
+        const adversarialTemplate = adversarialSkill?.promptTemplate ?? "";
+        const reviewPrompt = buildAdversarialPrompt(spec, adversarialTemplate);
+        const reviewAgent = new Agent({ config, learnings: learningsStr });
+        const response = await reviewAgent.run(reviewPrompt, { modelOverride: adversarialModel });
+        const verdict = response.includes("VERDICT: CHALLENGED")
+            ? "CHALLENGED"
+            : response.includes("NEEDS_CLARIFICATION")
+                ? "NEEDS_CLARIFICATION"
+                : "APPROVED";
+        logger.log({ event: "plan_review_completed", verdict, response });
+        if (verdict !== "APPROVED") {
+            console.log(`\nSpec ${verdict} before execution. Adversarial review response:\n`);
+            console.log(response);
+            const result = {
+                success: false,
+                attempts: 0,
+                criteriaResults: {},
+                runLogPath: logger.close(),
+                summary: `Spec ${verdict} before execution.`,
+                durationMs: Date.now() - startMs,
+                challenged: true,
+                challengeResponse: response,
+            };
+            await maybeNotify(options, config, result, basename(specPath));
+            return result;
+        }
+        console.log("\nAdversarial review: APPROVED. Proceeding with execution.");
+    }
+    // -------------------------------------------------------------------------
+    // Main execution loop
+    // -------------------------------------------------------------------------
+    const agent = new Agent({ config, learnings: learningsStr });
+    let attempt = state.attempt;
     let subtasksToRun = spec.decomposition;
     let previousFailureContext;
     let criteriaResults = {};
     while (attempt < maxAttempts) {
         attempt++;
+        state.attempt = attempt;
+        logger.log({ event: "attempt_started", attempt });
         console.log(`\n${"=".repeat(50)}`);
         console.log(`Attempt ${attempt}/${maxAttempts}`);
         console.log("=".repeat(50));
         // Run sub-tasks through satori
-        for (const subtask of subtasksToRun) {
+        for (let i = 0; i < subtasksToRun.length; i++) {
+            const subtask = subtasksToRun[i];
+            // When resuming, find the original index of this sub-task in the full decomposition.
+            const globalIndex = spec.decomposition.indexOf(subtask);
+            const indexKey = String(globalIndex >= 0 ? globalIndex : i);
+            const priorResult = state.subTaskResults[indexKey];
+            // Skip sub-tasks already marked passed on a prior run.
+            if (priorResult?.status === "passed") {
+                console.log(`\nSkipping sub-task (already passed): ${subtask.name}`);
+                continue;
+            }
+            // Inject prior failure context if this sub-task failed before.
+            const priorFailureContext = priorResult?.status === "failed"
+                ? priorResult.failureContext
+                : previousFailureContext;
+            const numericIndex = globalIndex >= 0 ? globalIndex : i;
+            logger.log({ event: "subtask_started", attempt, index: numericIndex, name: subtask.name });
             console.log(`\nRunning sub-task: ${subtask.name}`);
-            const taskContext = buildSatoriContext(subtask, spec.constraints, previousFailureContext);
+            const taskContext = buildSatoriContext(subtask, spec.constraints, priorFailureContext);
             // Combine satori system instructions + task-specific context
             const effectivePrompt = satoriTemplate
                 ? `${satoriTemplate}\n\n## Task\n${taskContext}`
                 : taskContext;
-            await agent.run(effectivePrompt, {
-                modelOverride: satoriModel,
-                maxRetries: satoriRetries,
-                verifyCommand: spec.evalCommand,
-                onDelta: (chunk) => process.stdout.write(chunk),
-            });
+            // Capture satori output so we can store it as failureContext if needed.
+            const outputChunks = [];
+            let satoriError = null;
+            try {
+                await agent.run(effectivePrompt, {
+                    modelOverride: satoriModel,
+                    maxRetries: satoriRetries,
+                    verifyCommand: spec.evalCommand,
+                    onDelta: (chunk) => {
+                        process.stdout.write(chunk);
+                        outputChunks.push(chunk);
+                    },
+                });
+            }
+            catch (err) {
+                satoriError = err;
+            }
             process.stdout.write("\n");
+            const outputStr = outputChunks.join("");
+            const truncated = outputStr.slice(-FAILURE_CONTEXT_MAX_BYTES);
+            if (satoriError) {
+                // Sub-task threw — mark as failed, write checkpoint, continue.
+                state.subTaskResults[indexKey] = {
+                    status: "failed",
+                    failureContext: truncated,
+                    attempts: (priorResult?.attempts ?? 0) + 1,
+                };
+                state.lastUpdatedAt = new Date().toISOString();
+                writeState(specDir, specHash, state);
+                logger.log({ event: "subtask_completed", attempt, index: numericIndex, status: "failed", failureContext: truncated });
+                console.error(`\nSub-task failed: ${subtask.name}`);
+            }
+            else {
+                // Sub-task completed without throwing — mark as passed, write checkpoint.
+                state.subTaskResults[indexKey] = {
+                    status: "passed",
+                    completedAt: new Date().toISOString(),
+                };
+                state.lastUpdatedAt = new Date().toISOString();
+                writeState(specDir, specHash, state);
+                logger.log({ event: "subtask_completed", attempt, index: numericIndex, status: "passed" });
+            }
         }
         // Run evaluation
         console.log(`\nRunning evaluation: ${spec.evalCommand}`);
+        logger.log({ event: "eval_started", command: spec.evalCommand });
         const evalOutput = await runCommand(spec.evalCommand);
         console.log(evalOutput.slice(0, 1000) + (evalOutput.length > 1000 ? "\n[...truncated...]" : ""));
+        // Store first 2000 chars in log (enough for diagnostics, not overwhelming)
+        logger.log({ event: "eval_completed", output: evalOutput.slice(0, 2000) });
         // If no acceptance criteria, report raw output and exit
         if (spec.acceptanceCriteria.length === 0) {
             console.log("\nNo acceptance criteria defined. Eval output shown above.");
-            return { success: true, attempts: attempt, criteriaResults: {} };
+            logger.log({ event: "goal_completed", success: true, attempts: attempt });
+            const result = {
+                success: true,
+                attempts: attempt,
+                criteriaResults: {},
+                runLogPath: logger.close(),
+                summary: `Goal completed successfully after ${attempt} attempt(s).`,
+                durationMs: Date.now() - startMs,
+            };
+            await maybeNotify(options, config, result, basename(specPath));
+            return result;
         }
         // Check acceptance criteria
         criteriaResults = await checkCriteria(spec.acceptanceCriteria, evalOutput, agent);
         printCriteriaTable(criteriaResults);
         const failing = Object.entries(criteriaResults).filter(([, pass]) => !pass).map(([c]) => c);
+        logger.log({ event: "criteria_checked", results: criteriaResults, failing });
         if (failing.length === 0) {
             console.log(`\n✓ All acceptance criteria met after ${attempt} attempt(s).`);
-            return { success: true, attempts: attempt, criteriaResults };
+            // Clean completion: remove state so stale state doesn't block future runs.
+            clearState(specDir, specHash);
+            logger.log({ event: "goal_completed", success: true, attempts: attempt });
+            const result = {
+                success: true,
+                attempts: attempt,
+                criteriaResults,
+                runLogPath: logger.close(),
+                summary: `All criteria passed after ${attempt} attempt(s).`,
+                durationMs: Date.now() - startMs,
+            };
+            await maybeNotify(options, config, result, basename(specPath));
+            return result;
         }
         if (attempt < maxAttempts) {
             previousFailureContext = await analyzeFailures(failing, evalOutput, spec, agent);
             subtasksToRun = await identifyFailedSubtasks(failing, spec.decomposition, previousFailureContext, agent);
+            // Reset passed sub-tasks on the next attempt so they re-run in context of new failures.
+            // We only keep the state for cross-run resumability, not within the same goal invocation.
             console.log(`\nRetrying ${subtasksToRun.length} sub-task(s): ${subtasksToRun.map((s) => s.name).join(", ")}`);
         }
     }
     console.log(`\n✗ Goal not achieved after ${maxAttempts} attempts.`);
     console.log("Failing criteria:");
-    for (const [criterion, pass] of Object.entries(criteriaResults)) {
-        if (!pass)
-            console.log(`  ✗ ${criterion}`);
+    const failingFinal = Object.entries(criteriaResults).filter(([, pass]) => !pass).map(([c]) => c);
+    for (const criterion of failingFinal) {
+        console.log(`  ✗ ${criterion}`);
+    }
+    logger.log({ event: "goal_completed", success: false, attempts: maxAttempts });
+    const failResult = {
+        success: false,
+        attempts: maxAttempts,
+        criteriaResults,
+        runLogPath: logger.close(),
+        summary: `Goal failed after ${maxAttempts} attempts. ${failingFinal.length} criteria not met.`,
+        durationMs: Date.now() - startMs,
+    };
+    await maybeNotify(options, config, failResult, basename(specPath));
+    return failResult;
+}
+// ---------------------------------------------------------------------------
+// Notification helper
+// ---------------------------------------------------------------------------
+/**
+ * Send a post-run notification if the caller requested one.
+ * Errors are swallowed — notification failures never surface to the user.
+ */
+async function maybeNotify(options, config, result, specFile) {
+    if (!options.notify)
+        return;
+    const notifyOptions = typeof options.notify === "object"
+        ? options.notify
+        : {
+            mac: config.notify?.mac,
+            slack: config.notify?.slack,
+            discord: config.notify?.discord,
+            teams: config.notify?.teams,
+        };
+    const payload = buildNotifyPayload(specFile, result.success, result.attempts, result.challenged ?? false, result.durationMs);
+    try {
+        await sendNotification(payload, notifyOptions);
+    }
+    catch (err) {
+        console.error(`[phase2s notify] Notification failed: ${String(err)}`);
     }
-    return { success: false, attempts: maxAttempts, criteriaResults };
+}
+// ---------------------------------------------------------------------------
+// buildAdversarialPrompt
+// ---------------------------------------------------------------------------
+/**
+ * Build a pre-execution adversarial review prompt.
+ *
+ * Injects the spec's decomposition and acceptance criteria as the "plan" to
+ * challenge, then appends the adversarial SKILL.md template which instructs
+ * the model to review what came before it and emit a structured verdict.
+ */
+export function buildAdversarialPrompt(spec, adversarialTemplate) {
+    const decompositionLines = spec.decomposition
+        .map((t, i) => `${i + 1}. **${t.name}**: ${t.successCriteria}`)
+        .join("\n");
+    const criteriaLines = spec.acceptanceCriteria
+        .map((c, i) => `${i + 1}. ${c}`)
+        .join("\n");
+    const plan = [
+        `## Spec: ${spec.title}`,
+        "",
+        "### Problem",
+        spec.problemStatement,
+        "",
+        "### Sub-task decomposition",
+        decompositionLines || "(none)",
+        "",
+        "### Acceptance criteria",
+        criteriaLines || "(none)",
+    ].join("\n");
+    return adversarialTemplate
+        ? `${plan}\n\n${adversarialTemplate}`
+        : plan;
 }
 // ---------------------------------------------------------------------------
 // Helpers

package/dist/src/cli/goal.js.map

@@ -1 +1 @@
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package/dist/src/cli/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/cli/index.ts"],"names":[],"mappings":"AAiEA,wBAAsB,IAAI,CAAC,IAAI,GAAE,MAAM,EAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyIvE;AAkfD;;;;;;;;GAQG;AACH,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,OAAO,oBAAoB,EAAE,KAAK,EAAE,GAC3C;IAAE,eAAe,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,GAAG,SAAS,CAAC;IAAC,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAAC,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAA;CAAE,CA6BjI"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/cli/index.ts"],"names":[],"mappings":"AAiEA,wBAAsB,IAAI,CAAC,IAAI,GAAE,MAAM,EAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4PvE;AAwfD;;;;;;;;GAQG;AACH,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,OAAO,oBAAoB,EAAE,KAAK,EAAE,GAC3C;IAAE,eAAe,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,GAAG,SAAS,CAAC;IAAC,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IAAC,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAA;CAAE,CA6BjI"}

package/dist/src/cli/index.js

@@ -124,11 +124,16 @@ export async function main(argv = process.argv) {
     });
     // List available skills
     program
-        .command("skills")
-        .description("List available skills")
+        .command("skills [query]")
+        .description("List available skills, or filter with an optional search query")
         .option("--json", "Output as JSON")
-        .action(async (cmdOpts) => {
-        const skills = await loadAllSkills();
+        .action(async (query, cmdOpts) => {
+        let skills = await loadAllSkills();
+        if (query) {
+            const q = query.toLowerCase();
+            skills = skills.filter((s) => s.name.toLowerCase().includes(q) ||
+                (s.description?.toLowerCase().includes(q) ?? false));
+        }
         if (cmdOpts.json) {
             const output = skills.map((s) => ({
                 name: s.name,
@@ -145,10 +150,18 @@ export async function main(argv = process.argv) {
             return;
         }
         if (skills.length === 0) {
-            log.info("No skills found. Add skills to .phase2s/skills/ or ~/.phase2s/skills/");
+            if (query) {
+                console.log(chalk.yellow(`\n  No skills match "${query}". Try a broader term or run phase2s skills to list all.\n`));
+            }
+            else {
+                log.info("No skills found. Add skills to .phase2s/skills/ or ~/.phase2s/skills/");
+            }
             return;
         }
-        console.log(chalk.bold("\nAvailable skills:\n"));
+        const header = query
+            ? chalk.bold(`\nSkills matching "${query}":\n`)
+            : chalk.bold("\nAvailable skills:\n");
+        console.log(header);
         for (const skill of skills) {
             const tierBadge = skill.model === "fast"
                 ? chalk.blue(" [fast]")
@@ -164,10 +177,98 @@ export async function main(argv = process.argv) {
         .command("goal <spec-file>")
         .description("Execute a spec file end-to-end: run sub-tasks, evaluate, retry until done")
         .option("--max-attempts <n>", "Maximum retry loops (default: 3)", "3")
+        .option("--resume", "Resume from the last completed sub-task (reads state from .phase2s/state/)")
+        .option("--review-before-run", "Run adversarial review on spec before executing")
+        .option("--notify", "Send a notification when the run completes (macOS + optional Slack webhook)")
         .action(async (specFile, cmdOpts) => {
         const { runGoal } = await import("./goal.js");
-        const result = await runGoal(specFile, { maxAttempts: cmdOpts.maxAttempts });
-        process.exit(result.success ? 0 : 1);
+        try {
+            const result = await runGoal(specFile, {
+                maxAttempts: cmdOpts.maxAttempts,
+                resume: cmdOpts.resume,
+                reviewBeforeRun: cmdOpts.reviewBeforeRun,
+                notify: cmdOpts.notify,
+            });
+            if (result.runLogPath)
+                console.log(`Run log: ${result.runLogPath}`);
+            process.exit(result.success ? 0 : 1);
+        }
+        catch (err) {
+            console.error(err instanceof Error ? err.message : String(err));
+            process.exit(1);
+        }
+    });
+    // Run log report viewer
+    program
+        .command("report <logfile>")
+        .description("Display a human-readable summary of a dark factory run log (.jsonl)")
+        .action(async (logfile) => {
+        const { parseRunLog, buildRunReport, formatRunReport } = await import("./report.js");
+        try {
+            const events = parseRunLog(logfile);
+            const report = buildRunReport(events);
+            console.log(formatRunReport(report));
+        }
+        catch (err) {
+            console.error(`Error reading run log: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    // Interactive setup wizard
+    program
+        .command("init")
+        .description("Interactive setup wizard — configure .phase2s.yaml for your provider")
+        .option("--non-interactive", "Skip prompts and use flag values (for CI)")
+        .option("--provider <provider>", "Provider: codex-cli, openai-api, anthropic, ollama, openrouter, gemini")
+        .option("--api-key <key>", "API key for openai-api or anthropic provider")
+        .option("--openrouter-api-key <key>", "API key for openrouter provider")
+        .option("--gemini-api-key <key>", "API key for gemini provider (starts with AIza)")
+        .option("--fast-model <model>", "Fast tier model name")
+        .option("--smart-model <model>", "Smart tier model name")
+        .option("--slack-webhook <url>", "Slack webhook URL for notifications")
+        .option("--discord-webhook <url>", "Discord webhook URL for notifications")
+        .option("--teams-webhook <url>", "Microsoft Teams webhook URL for notifications")
+        .action(async (cmdOpts) => {
+        const { runInit } = await import("./init.js");
+        await runInit({
+            nonInteractive: cmdOpts.nonInteractive,
+            provider: cmdOpts.provider,
+            apiKey: cmdOpts.apiKey,
+            openrouterApiKey: cmdOpts.openrouterApiKey,
+            geminiApiKey: cmdOpts.geminiApiKey,
+            fastModel: cmdOpts.fastModel,
+            smartModel: cmdOpts.smartModel,
+            slackWebhook: cmdOpts.slackWebhook,
+            discordWebhook: cmdOpts.discordWebhook,
+            teamsWebhook: cmdOpts.teamsWebhook,
+        });
+    });
+    // Self-update command
+    program
+        .command("upgrade")
+        .description("Check for a newer version and offer to install it")
+        .option("--check", "Report whether an update is available without prompting")
+        .action(async (cmdOpts) => {
+        const { runUpgrade } = await import("./upgrade.js");
+        await runUpgrade(VERSION, { check: cmdOpts.check });
+    });
+    // Spec linting
+    program
+        .command("lint <spec-file>")
+        .description("Validate a 5-pillar spec file before running it — catches structural errors before the dark factory run begins")
+        .action(async (specFile) => {
+        const { runLint } = await import("./lint.js");
+        const ok = await runLint(specFile);
+        if (!ok)
+            process.exit(1);
+    });
+    // Installation health check
+    program
+        .command("doctor")
+        .description("Check Phase2S installation health — Node version, auth, config, working dir")
+        .action(async () => {
+        const { runDoctor } = await import("./doctor.js");
+        await runDoctor();
     });
     // Shell completion script generator
     program
@@ -202,7 +303,7 @@ _phase2s_complete() {
 
   # Complete subcommands at position 1
   if [[ \${COMP_CWORD} -eq 1 ]]; then
-    COMPREPLY=($(compgen -W "chat run skills mcp completion" -- "\$cur"))
+    COMPREPLY=($(compgen -W "chat run skills mcp goal report init upgrade lint doctor completion" -- "\$cur"))
     return
   fi
 
@@ -238,6 +339,12 @@ _phase2s() {
     'run:Run a single prompt and exit'
     'skills:List available skills'
     'mcp:Start as an MCP server for Claude Code'
+    'goal:Run a spec file autonomously (dark factory)'
+    'report:Display a human-readable summary of a run log'
+    'init:Interactive setup wizard — configure .phase2s.yaml'
+    'upgrade:Check for a newer version and offer to install it'
+    'lint:Validate a 5-pillar spec file before running it'
+    'doctor:Check Phase2S installation health'
     'completion:Output shell completion script'
   )