agent-bober 0.17.1 → 0.19.0

package/dist/cli/commands/research.js

@@ -0,0 +1,313 @@
+/**
+ * `agent-bober research job add|list|remove` — manage recurring multi-model research jobs.
+ * `agent-bober research run <jobId>`         — execute a stored research job.
+ * `agent-bober research tick [--watch]`      — run every due job (idempotent).
+ *
+ * Subcommands:
+ *   research job add --question "..." [--cadence daily|weekly|monthly] [--tier <t>]
+ *                    [--domain <d>] [--target-repo <r>] [--online-research]
+ *   research job list
+ *   research job remove <jobId>
+ *   research run <jobId>
+ *   research tick [--watch] [--interval <ms>]
+ *
+ * Error handling: CLI handlers MUST NOT throw. They set process.exitCode=1 and
+ * return on all errors. Pattern mirrors src/cli/commands/task.ts:360-367.
+ *
+ * Clock discipline: new Date().toISOString() is called ONLY at the .action()
+ * boundary — never inside the store (mirrors task.ts:352 "stamp wall-clock time
+ * at handler boundary").
+ *
+ * fs boundary: ALL direct fs work (ensureDir, writeFile) happens inside runner.ts
+ * and note-writer.ts. This file only calls readJob (JSON read) and opens FactStore.
+ * This keeps the utils/fs.js import surface minimal (only findProjectRoot) so that
+ * the research.test.ts whole-module vi.mock of utils/fs.js stays stable.
+ */
+import chalk from "chalk";
+import { join } from "node:path";
+import { findProjectRoot } from "../../utils/fs.js";
+import { buildDigest, collectRunsFromVault } from "../../research/digest.js";
+import { addJob, listJobs, removeJob, jobId, readJob, } from "../../research/job-store.js";
+import { ResearchJobSchema } from "../../research/types.js";
+import { FactStore, factsDbPath, ensureFactsDir, } from "../../state/facts.js";
+import { ingestFinding } from "../../hub/finding-store.js";
+import { runResearchJob } from "../../research/runner.js";
+import { tick } from "../../research/scheduler.js";
+import { createClient } from "../../providers/factory.js";
+// ── Root resolver ─────────────────────────────────────────────────────
+async function resolveRoot() {
+    const root = await findProjectRoot();
+    return root ?? process.cwd();
+}
+// ── registerResearchCommand ───────────────────────────────────────────
+export function registerResearchCommand(program, overrides) {
+    const researchCmd = program
+        .command("research")
+        .description("Recurring multi-model research jobs");
+    const jobCmd = researchCmd
+        .command("job")
+        .description("Define and manage recurring research jobs (JSON store under .bober/research/jobs)");
+    // ── research job add ─────────────────────────────────────────────
+    jobCmd
+        .command("add")
+        .description("Add a recurring research job")
+        .requiredOption("--question <q>", "The research question (non-empty)")
+        .option("--cadence <c>", "Recurrence cadence: daily | weekly | monthly", "weekly")
+        .option("--tier <t>", "Difficulty tier hint (e.g. hard) — used by executor (Sprint 2)")
+        .option("--domain <d>", "Domain tag (e.g. medical, coding)")
+        .option("--target-repo <r>", "Repository slug to scope the research against")
+        .option("--online-research", "Store onlineResearch=true (egress is not active until Sprint 3)")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        try {
+            // Stamp wall-clock time ONLY here — never inside the store
+            const now = new Date().toISOString();
+            const id = jobId(opts.question, now);
+            const job = ResearchJobSchema.parse({
+                id,
+                question: opts.question,
+                cadence: opts.cadence ?? "weekly",
+                tier: opts.tier,
+                domain: opts.domain,
+                targetRepo: opts.targetRepo,
+                onlineResearch: opts.onlineResearch ?? false,
+                createdAt: now,
+            });
+            await addJob(projectRoot, job);
+            process.stdout.write(chalk.green(`Added research job ${chalk.bold(job.id)}\n`) +
+                `  question: ${job.question}\n` +
+                `  cadence:  ${job.cadence}\n`);
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`research job add failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+    // ── research job list ────────────────────────────────────────────
+    jobCmd
+        .command("list")
+        .description("List all recurring research jobs")
+        .action(async () => {
+        const projectRoot = await resolveRoot();
+        try {
+            const jobs = await listJobs(projectRoot);
+            if (jobs.length === 0) {
+                process.stdout.write("No research jobs defined.\n");
+                return;
+            }
+            for (const job of jobs) {
+                process.stdout.write(`${chalk.bold(job.id)}  ${job.cadence}  ${job.question}` +
+                    (job.domain ? `  [${job.domain}]` : "") +
+                    "\n");
+            }
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`research job list failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+    // ── research job remove ──────────────────────────────────────────
+    jobCmd
+        .command("remove <jobId>")
+        .description("Remove a recurring research job by id")
+        .action(async (id) => {
+        const projectRoot = await resolveRoot();
+        try {
+            const removed = await removeJob(projectRoot, id);
+            if (removed) {
+                process.stdout.write(chalk.green(`Removed research job ${chalk.bold(id)}\n`));
+            }
+            else {
+                process.stderr.write(chalk.yellow(`Research job not found: ${id}\n`));
+                process.exitCode = 1;
+            }
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`research job remove failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+    // ── research run <jobId> ─────────────────────────────────────────
+    researchCmd
+        .command("run <jobId>")
+        .description("Execute a stored research job: query >=2 model blocks, write a vault note, emit a hub Finding")
+        .action(async (id) => {
+        const projectRoot = await resolveRoot();
+        try {
+            const job = await readJob(projectRoot, id);
+            if (job === null) {
+                process.stderr.write(chalk.red(`Research job not found: ${id}\n`));
+                process.exitCode = 1;
+                return;
+            }
+            // Stamp wall-clock time ONLY at the handler boundary (principles L31)
+            const now = new Date().toISOString();
+            // Vault root: default to projectRoot (same pattern as `bober vault reindex`)
+            const vaultRoot = projectRoot;
+            // -- queryModel binding --
+            // Use override (tests) or build a real provider-agnostic client binding.
+            // createClient is the ONLY place where provider SDKs are imported — never here.
+            const qm = overrides?.queryModel ??
+                ((block, prompt) => {
+                    const client = createClient(block.provider, block.endpoint ?? null, undefined, block.model, "research");
+                    return client
+                        .chat({
+                        model: block.model,
+                        system: "You are a research assistant. Answer concisely and accurately.",
+                        messages: [{ role: "user", content: prompt }],
+                    })
+                        .then((r) => r.text);
+                });
+            // -- findingSink binding --
+            // Use override (tests) or bind to the real hub ingestFinding.
+            let store = null;
+            const fs = overrides?.findingSink ??
+                (async (finding) => {
+                    if (store === null) {
+                        throw new Error("FactStore was closed before findingSink was called");
+                    }
+                    await ingestFinding(store, finding, { now });
+                });
+            if (overrides?.findingSink === undefined) {
+                await ensureFactsDir(projectRoot);
+                store = new FactStore(factsDbPath(projectRoot));
+            }
+            try {
+                const res = await runResearchJob(job, {
+                    queryModel: qm,
+                    findingSink: fs,
+                    now,
+                    vaultRoot,
+                });
+                process.stdout.write(res.notePath + "\n");
+            }
+            finally {
+                store?.close();
+            }
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`research run failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+    // ── research tick [--watch] ──────────────────────────────────────────
+    researchCmd
+        .command("tick")
+        .description("Run every research job that is due as of now (idempotent).\n\n" +
+        "Scheduling mechanism tradeoff:\n" +
+        "  --watch        in-process setInterval loop — simple, but DIES with the\n" +
+        "                 process (not suitable for unattended production use).\n" +
+        "  OS cron/launchd calling `agent-bober research tick` — survives reboots;\n" +
+        "                 RECOMMENDED for unattended runs. Example crontab entry:\n" +
+        "                   0 * * * * /usr/local/bin/agent-bober research tick\n" +
+        "  harness scheduler (/schedule) — fires the CLI on a cadence inside the\n" +
+        "                 agent harness.\n\n" +
+        "Note: hosted-OAuth schedulers are unfit for unattended runs (research\n" +
+        "doc L135) — use OS cron/launchd for unattended scheduling.")
+        .option("--watch", "Run tick on an in-process interval (loop keeps process alive)")
+        .option("--interval <ms>", "Watch interval in milliseconds (default: 3600000 = 1 hour)", "3600000")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        const vaultRoot = projectRoot;
+        // Build one runOnce closure that captures the injected deps.
+        // clock is stamped ONLY inside runOnce at the .action boundary.
+        const runOnce = async () => {
+            // Wall-clock read happens ONLY here (principles L31 / research.ts clock discipline).
+            const now = new Date().toISOString();
+            // -- queryModel binding (mirrors research run above) --
+            const qm = overrides?.queryModel ??
+                ((block, prompt) => {
+                    const client = createClient(block.provider, block.endpoint ?? null, undefined, block.model, "research");
+                    return client
+                        .chat({
+                        model: block.model,
+                        system: "You are a research assistant. Answer concisely and accurately.",
+                        messages: [{ role: "user", content: prompt }],
+                    })
+                        .then((r) => r.text);
+                });
+            // -- findingSink binding (open/close FactStore per runOnce for --watch) --
+            let store = null;
+            const fs = overrides?.findingSink ??
+                (async (finding) => {
+                    if (store === null) {
+                        throw new Error("FactStore was closed before findingSink was called");
+                    }
+                    await ingestFinding(store, finding, { now });
+                });
+            if (overrides?.findingSink === undefined) {
+                await ensureFactsDir(projectRoot);
+                store = new FactStore(factsDbPath(projectRoot));
+            }
+            try {
+                const result = await tick({
+                    now,
+                    listJobs: () => listJobs(projectRoot),
+                    saveJob: (j) => addJob(projectRoot, j),
+                    runJob: (job) => runResearchJob(job, {
+                        queryModel: qm,
+                        findingSink: fs,
+                        now,
+                        vaultRoot,
+                    }).then(() => undefined),
+                });
+                if (result.ran.length > 0) {
+                    process.stdout.write(chalk.green(`research tick: ran ${result.ran.length} job(s): ${result.ran.join(", ")}\n`));
+                }
+                else {
+                    process.stdout.write("research tick: no jobs due.\n");
+                }
+            }
+            finally {
+                // Always close the store — prevents SQLite lock across interval iterations.
+                store?.close();
+            }
+        };
+        try {
+            await runOnce();
+            if (opts.watch === true) {
+                const ms = Math.max(1000, Number(opts.interval ?? "3600000"));
+                // Do NOT .unref() — the watch loop must keep the process alive.
+                // bober: in-memory setInterval; replace with OS cron if the process must
+                //        survive reboots or system sleep (contract nonGoal L4 / briefing §9).
+                setInterval(() => {
+                    void runOnce();
+                }, ms);
+            }
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`research tick failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+    // ── research digest [--since <iso>] ─────────────────────────────────
+    researchCmd
+        .command("digest")
+        .description("Aggregate research runs in [since, now] into a dual md+json digest artifact.\n\n" +
+        "Writes .bober/research/digests/<YYYY-MM-DD>.{md,json} under the project root.\n" +
+        "Empty window: emits an explicit no-new-research digest — never throws.\n" +
+        "Consumer: the Telegram bot (sibling spec) reads the JSON for silent scheduled messages.")
+        .option("--since <iso>", "Window start ISO string (default: 24h before now)")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        try {
+            // Stamp wall-clock ONLY here — never inside digest.ts (clock discipline)
+            const now = new Date().toISOString();
+            const since = opts.since ?? new Date(Date.now() - 24 * 60 * 60 * 1000).toISOString();
+            const vaultRoot = projectRoot; // same default as `research run`
+            const digestsDir = join(projectRoot, ".bober", "research", "digests");
+            const res = await buildDigest(since, now, {
+                // Use injected collector (tests) or real vault-note reader (production)
+                collectRuns: overrides?.digestCollectRuns ??
+                    ((s, n) => collectRunsFromVault(vaultRoot, s, n)),
+                digestsDir,
+            });
+            process.stdout.write(res.mdPath + "\n" + res.jsonPath + "\n");
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`research digest failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+}
+//# sourceMappingURL=research.js.map

package/dist/cli/commands/research.js.map

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package/dist/cli/commands/run.d.ts

@@ -1,3 +1,6 @@
+import type { CheckpointId } from "../../orchestrator/checkpoints/types.js";
+/** Valid --approve-gates names — sourced from the declared checkpoint sites. */
+export declare const KNOWN_CHECKPOINT_IDS: readonly CheckpointId[];
 export interface RunCommandOptions {
     verbose?: boolean;
     /** Override AI provider for all roles. Overrides config.planner/generator/evaluator.provider. */
@@ -11,6 +14,12 @@ export interface RunCommandOptions {
      *  Without this flag, --checkpoint only overrides the global default; per-checkpoint
      *  overrides in config still win. With this flag, --checkpoint wins everywhere. */
     checkpointAll?: boolean;
+    /** When set, the pipeline honors this runId instead of self-generating run-<timestamp>. */
+    runId?: string;
+    /** When set, selects the active team; absent => config.defaultTeam then 'programming'. */
+    team?: string;
+    /** Comma-separated checkpoint ids to gate via the 'disk' mechanism for this run only. */
+    approveGates?: string;
 }
 export declare function runRunCommand(taskDescription: string | undefined, projectRoot: string, options: RunCommandOptions): Promise<void>;
 //# sourceMappingURL=run.d.ts.map

package/dist/cli/commands/run.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/run.ts"],"names":[],"mappings":"AAUA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,yCAAyC,CAAC;AAG5E,gFAAgF;AAChF,eAAO,MAAM,oBAAoB,EAAE,SAAS,YAAY,EACrB,CAAC;AAIpC,MAAM,WAAW,iBAAiB;IAChC,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,iGAAiG;IACjG,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,+EAA+E;IAC/E,IAAI,CAAC,EAAE,WAAW,GAAG,SAAS,CAAC;IAC/B;sFACkF;IAClF,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB;;uFAEmF;IACnF,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,2FAA2F;IAC3F,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,0FAA0F;IAC1F,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,yFAAyF;IACzF,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAeD,wBAAsB,aAAa,CACjC,eAAe,EAAE,MAAM,GAAG,SAAS,EACnC,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,iBAAiB,GACzB,OAAO,CAAC,IAAI,CAAC,CAsMf"}

package/dist/cli/commands/run.js

@@ -6,6 +6,10 @@ import { configExists } from "../../config/loader.js";
 import { runPipeline } from "../../orchestrator/pipeline.js";
 import { ensureBoberDir } from "../../state/index.js";
 import { logger } from "../../utils/logger.js";
+import { CHECKPOINT_SITES } from "../../orchestrator/checkpoints/sites.js";
+// ── Valid approve-gate ids — sourced from the declared checkpoint sites ──
+/** Valid --approve-gates names — sourced from the declared checkpoint sites. */
+export const KNOWN_CHECKPOINT_IDS = CHECKPOINT_SITES.map((s) => s.id);
 // ── Formatting helpers ─────────────────────────────────────────────
 function formatDuration(ms) {
     if (ms < 1000)
@@ -92,6 +96,22 @@ export async function runRunCommand(taskDescription, projectRoot, options) {
         };
         logger.info(`Checkpoint override: ${options.checkpoint}`);
     }
+    // Apply --approve-gates: merge { gate -> 'disk' } into checkpointOverrides for this run only.
+    if (options.approveGates) {
+        const gates = options.approveGates.split(",").map((g) => g.trim()).filter(Boolean);
+        const unknown = gates.filter((g) => !KNOWN_CHECKPOINT_IDS.includes(g));
+        if (unknown.length > 0) {
+            logger.error(`Unknown approve-gate(s): ${unknown.join(", ")}. ` +
+                `Valid gates: ${KNOWN_CHECKPOINT_IDS.join(", ")}.`);
+            process.exitCode = 1;
+            return; // do not apply a partial merge
+        }
+        const merged = { ...config.pipeline.checkpointOverrides };
+        for (const g of gates)
+            merged[g] = "disk";
+        config = { ...config, pipeline: { ...config.pipeline, checkpointOverrides: merged } };
+        logger.info(`Approve-gates: ${gates.join(", ")} -> disk`);
+    }
     // Ensure .bober directory
     await ensureBoberDir(projectRoot);
     // Show start banner
@@ -104,7 +124,13 @@ export async function runRunCommand(taskDescription, projectRoot, options) {
     const spinner = ora("Starting pipeline...").start();
     try {
         spinner.stop();
-        const result = await runPipeline(task, projectRoot, config);
+        if (options.team) {
+            logger.info(`Team: ${options.team}`);
+        }
+        const result = await runPipeline(task, projectRoot, config, {
+            runId: options.runId,
+            teamId: options.team,
+        });
         // Display final summary
         console.log();
         console.log(chalk.bold("═══ Pipeline Summary ═══"));

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package/dist/cli/commands/security-audit.d.ts

@@ -0,0 +1,89 @@
+/**
+ * `agent-bober security-audit [target]` — on-demand stack-aware security audit.
+ *
+ * Synthesizes a lightweight SprintContract-shaped descriptor from the target
+ * path (or the working tree when omitted), runs the same `runSecurityAudit`
+ * core the in-pipeline gate uses (with `evaluation=null` for standalone
+ * mode), persists the artifact via `saveSecurityAudit` (called internally by
+ * the core), prints a human-readable findings summary, and exits with a
+ * CI-friendly code driven by `security.standaloneBlockOn`.
+ *
+ * Threshold semantics (sc-4-2) are CLI-local by design: `thresholdVerdict`
+ * lives HERE, never in `security-gate.ts`. The pipeline gate's critical-only
+ * veto (ADR-2) stays structurally untouched — this command reads
+ * `security.standaloneBlockOn` to decide its OWN exit code only.
+ *
+ * Exit codes: 0 = pass, 2 = blocked-by-threshold OR fail-closed (audit threw,
+ * or the auditor's output could not be parsed). 1 is reserved for Commander's
+ * own usage errors and for unexpected errors resolving config/project root.
+ *
+ * Clock discipline: `new Date().toISOString()` is called ONLY at the
+ * `.action()` boundary — never inside `runStandaloneSecurityAudit` — mirrors
+ * `research.ts`'s "stamp wall-clock time at handler boundary" convention.
+ * Hub emission (sprint 6) reuses `deps.now` for the same reason — it is
+ * never re-stamped inside this module.
+ *
+ * Error handling: CLI handlers MUST NOT throw. They set `process.exitCode`
+ * and return on all errors (mirrors `research.ts` / `do.ts`).
+ */
+import type { Command } from "commander";
+import type { BoberConfig } from "../../config/schema.js";
+import type { SprintContract } from "../../contracts/sprint-contract.js";
+import type { ReviewResult } from "../../orchestrator/code-reviewer-agent.js";
+import type { SecurityAuditResult } from "../../orchestrator/security-audit-types.js";
+import { runSecurityAudit } from "../../orchestrator/security-auditor-agent.js";
+import type { SecurityFindingSink } from "../../orchestrator/security-hub.js";
+/**
+ * Decide whether the standalone CLI should block (exit 2) given a review and
+ * the configured `standaloneBlockOn` threshold. Pure function — no I/O.
+ *
+ * `critical` findings always block, regardless of threshold. `important`
+ * findings only block when `standaloneBlockOn === "important"`. `minor`
+ * findings never block. This is intentionally a *superset* of the pipeline
+ * gate's critical-only veto (`deriveVerdict`) — it must never be imported
+ * into `security-gate.ts` or `pipeline.ts` (sc-4-4 is verified structurally).
+ */
+export declare function thresholdVerdict(review: ReviewResult, standaloneBlockOn: "critical" | "important"): boolean;
+/**
+ * Build a synthetic SprintContract-shaped descriptor for the standalone
+ * audit. The `contractId` is timestamped (`security-audit-<slug>`) so it can
+ * never collide with a pipeline sprint's `sprint-*` contractId, and so the
+ * fs-safe sanitization in `security-audit-state.ts` produces a stable,
+ * readable artifact filename.
+ */
+export declare function buildAuditDescriptor(target: string | undefined, now: string): SprintContract;
+/** Injectable deps so tests never spawn a process or hit a real provider. */
+export interface StandaloneAuditDeps {
+    projectRoot: string;
+    config: BoberConfig;
+    target?: string;
+    /** ISO timestamp, stamped ONCE at the `.action` boundary. */
+    now: string;
+    /** Default = the real `runSecurityAudit` core; tests inject a fake. */
+    runAudit?: typeof runSecurityAudit;
+    /** Injected hub sink (tests only) — default binds ingestFinding to a real FactStore. */
+    findingSink?: SecurityFindingSink;
+}
+export interface StandaloneAuditOutcome {
+    result?: SecurityAuditResult;
+    exitCode: 0 | 2;
+}
+/**
+ * Run a standalone security audit and compute the CI exit code.
+ *
+ * `config.security` may be absent — that is legal for standalone mode (the
+ * explicit CLI invocation IS the opt-in; nonGoals[0]). When absent, the
+ * section is synthesized via `SecuritySectionSchema.parse({})` so the audit
+ * still runs with schema defaults (sc-4-3).
+ *
+ * Fail-closed (sc-4-2): a thrown audit error, or `result.parsed === false`,
+ * always exits 2 — checked BEFORE the threshold, so an empty fallback review
+ * (which `thresholdVerdict` alone would read as "clean") never yields a
+ * false pass.
+ */
+export declare function runStandaloneSecurityAudit(deps: StandaloneAuditDeps): Promise<StandaloneAuditOutcome>;
+export interface SecurityAuditOverrides {
+    runAudit?: typeof runSecurityAudit;
+}
+export declare function registerSecurityAuditCommand(program: Command, overrides?: SecurityAuditOverrides): void;
+//# sourceMappingURL=security-audit.d.ts.map

package/dist/cli/commands/security-audit.d.ts.map

@@ -0,0 +1 @@
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