@jokerized/getresearchdone 0.4.1

package/dist/lib/commands/patterns.js

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+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isConfirmed = isConfirmed;
+exports.scanReflections = scanReflections;
+exports.binomTwoSidedP = binomTwoSidedP;
+exports.benjaminiHochberg = benjaminiHochberg;
+exports.computeTokenStats = computeTokenStats;
+exports.cmdPatterns = cmdPatterns;
+/**
+ * GRD Commands/Patterns — v0.4 Phase 5 deterministic pattern extractor.
+ *
+ * Scans VERIFICATION.md `<reflection>` blocks, computes per-token verdict
+ * statistics over each plan's PLAN.md vocabulary, and *suggests*
+ * statistically significant heuristics for human review. The defensible
+ * fraction of the meta-review-agent idea that DEAD-ENDS rules out
+ * (`meta-review-agent-with-write-access`): same data source (reflections),
+ * same goal (compound learnings into GENOME), but the write path is
+ * deterministic statistics + human review, NOT LLM judgment.
+ *
+ * Statistical floor — a token is "significant" only if ALL hold:
+ *   (a) appears in >= min_occurrences plans (default 10)
+ *   (b) |confirmed_rate - baseline| >= effect_size (default 0.20)
+ *   (c) raw two-sided binomial p < 0.05 against the baseline rate
+ *   (d) Benjamini-Hochberg FDR-corrected q < fdr_q (default 0.10)
+ *
+ * (b)+(d) are the codex r-bkknb6i9g P2 #7 additions: a bare per-token
+ * p<0.05 across many tokens invites multiple-comparison noise.
+ *
+ * Output: suggestions go to .planning/GENOME-SUGGESTIONS.md (a SEPARATE
+ * file — codex P1 #5 + DEAD-ENDS slug `auto-suggestions-in-genome-file`).
+ * GENOME.md is NEVER written here; promotion is the human-curated
+ * `gd genome promote-suggestion <slug>`. --dry-run is the default;
+ * --apply requires --yes. No autopilot integration, no LLM round-trip.
+ */
+const fs = require('fs');
+const path = require('path');
+const { safeReadMarkdown, output, error, } = require('../utils');
+const { atomicWriteFileSync, } = require('../autopilot-waves');
+// ─── Tokenisation ───────────────────────────────────────────────────────────
+/**
+ * Low-information implementation tokens suppressed from pattern mining —
+ * they appear in nearly every plan and carry no strategy signal. Combines
+ * generic English stopwords with TypeScript/JS implementation keywords.
+ */
+const STOPWORDS = new Set([
+    // generic (mirrors lib/drift.ts + plan-tournament.ts)
+    'the', 'and', 'for', 'with', 'from', 'into', 'over', 'this', 'that',
+    'are', 'was', 'were', 'has', 'have', 'had', 'will', 'would', 'should',
+    'phase', 'plan', 'summary', 'roadmap', 'task', 'goal',
+    // implementation keywords (codex P2 #7: suppress low-information tokens)
+    'function', 'const', 'let', 'var', 'import', 'export', 'return', 'async',
+    'await', 'type', 'interface', 'class', 'module', 'require', 'test', 'tests',
+    'unit', 'integration', 'file', 'files', 'code', 'add', 'added', 'update',
+    'implement', 'use', 'using', 'new',
+]);
+function tokenize(text) {
+    const set = new Set();
+    const matches = text.toLowerCase().match(/[a-z0-9][a-z0-9_-]{2,}/g);
+    if (!matches)
+        return set;
+    for (const t of matches) {
+        if (STOPWORDS.has(t))
+            continue;
+        set.add(t);
+    }
+    return set;
+}
+// ─── Reflection scanning ──────────────────────────────────────────────────
+/**
+ * True when a verdict string asserts the hypothesis held. Reflection
+ * verdicts are `confirmed | falsified | partial` (and variants). Anything
+ * that isn't an affirmative confirmation counts as not-confirmed.
+ */
+function isConfirmed(verdict) {
+    const v = verdict.trim().toLowerCase();
+    if (/\b(not|un)[\s-]?confirmed\b/.test(v))
+        return false;
+    return /\b(confirmed|validated|pass(ed)?|holds?|supported|true)\b/.test(v);
+}
+function extractVerdict(reflectionYaml) {
+    const m = reflectionYaml.match(/^\s*verdict:\s*["']?([^"'\n]+?)["']?\s*$/m);
+    return m ? m[1].trim() : null;
+}
+/**
+ * Scan all VERIFICATION.md files under .planning/milestones (and a bare
+ * top-level VERIFICATION.md) for `<reflection>` blocks carrying a verdict.
+ * Each reflection's plan vocabulary comes from the sibling PLAN.md.
+ *
+ * Uses safeReadMarkdown so GRD-INDEX split-format files reassemble (GENOME
+ * heuristic). Returns one Reflection per verdict-bearing block found.
+ */
+function scanReflections(cwd) {
+    const reflections = [];
+    const planningDir = path.join(cwd, '.planning');
+    const verificationFiles = findVerificationFiles(planningDir);
+    for (const vf of verificationFiles) {
+        const content = safeReadMarkdown(vf);
+        if (!content)
+            continue;
+        // Parent-dir PLAN.md vocabulary (prefer resolved PLAN.md, else PLAN-1.md).
+        const dir = path.dirname(vf);
+        const planContent = readSiblingPlan(dir);
+        const vocabulary = planContent ? tokenize(planContent) : new Set();
+        for (const block of extractReflectionBlocks(content)) {
+            const verdict = extractVerdict(block);
+            if (!verdict)
+                continue;
+            reflections.push({
+                source: path.relative(cwd, vf),
+                verdict,
+                confirmed: isConfirmed(verdict),
+                vocabulary,
+            });
+        }
+    }
+    return reflections;
+}
+function findVerificationFiles(planningDir) {
+    const out = [];
+    const bare = path.join(planningDir, 'VERIFICATION.md');
+    if (fileExists(bare))
+        out.push(bare);
+    const milestonesDir = path.join(planningDir, 'milestones');
+    // .planning/milestones/<m>/phases/<p>/VERIFICATION.md (and bare/prefixed forms).
+    for (const milestone of listDirs(milestonesDir)) {
+        const phasesDir = path.join(milestonesDir, milestone, 'phases');
+        for (const phase of listDirs(phasesDir)) {
+            const phaseDir = path.join(phasesDir, phase);
+            for (const name of listFiles(phaseDir)) {
+                if (name === 'VERIFICATION.md' || /-VERIFICATION\.md$/.test(name)) {
+                    out.push(path.join(phaseDir, name));
+                }
+            }
+        }
+    }
+    return out;
+}
+function readSiblingPlan(dir) {
+    // Prefer the resolved PLAN.md; fall back to the first candidate.
+    const direct = path.join(dir, 'PLAN.md');
+    if (fileExists(direct))
+        return safeReadMarkdown(direct);
+    for (const name of listFiles(dir)) {
+        if (/^PLAN-\d+\.md$/.test(name) || /-PLAN\.md$/.test(name)) {
+            return safeReadMarkdown(path.join(dir, name));
+        }
+    }
+    return null;
+}
+function extractReflectionBlocks(content) {
+    // <reflection> ... </reflection> blocks; the YAML inside may be fenced.
+    const blocks = [];
+    const re = /<reflection>([\s\S]*?)<\/reflection>/g;
+    for (const m of content.matchAll(re))
+        blocks.push(m[1]);
+    return blocks;
+}
+function fileExists(p) {
+    try {
+        return fs.statSync(p).isFile();
+    }
+    catch {
+        return false;
+    }
+}
+function listDirs(p) {
+    try {
+        return fs
+            .readdirSync(p, { withFileTypes: true })
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name);
+    }
+    catch {
+        return [];
+    }
+}
+function listFiles(p) {
+    try {
+        return fs
+            .readdirSync(p, { withFileTypes: true })
+            .filter((e) => e.isFile())
+            .map((e) => e.name);
+    }
+    catch {
+        return [];
+    }
+}
+// ─── Binomial test + Benjamini-Hochberg FDR ─────────────────────────────────
+const _logFactCache = [0, 0];
+function logFactorial(n) {
+    for (let i = _logFactCache.length; i <= n; i++) {
+        _logFactCache[i] = _logFactCache[i - 1] + Math.log(i);
+    }
+    return _logFactCache[n];
+}
+function logChoose(n, k) {
+    return logFactorial(n) - logFactorial(k) - logFactorial(n - k);
+}
+function binomPmf(k, n, p) {
+    if (p <= 0)
+        return k === 0 ? 1 : 0;
+    if (p >= 1)
+        return k === n ? 1 : 0;
+    return Math.exp(logChoose(n, k) + k * Math.log(p) + (n - k) * Math.log(1 - p));
+}
+/**
+ * Two-sided exact binomial test p-value: the total probability of all
+ * outcomes no more likely than the observed count under the null rate p0
+ * (method of small p-values). Returns 1 when p0 is degenerate (0 or 1).
+ */
+function binomTwoSidedP(k, n, p0) {
+    if (n === 0)
+        return 1;
+    if (p0 <= 0 || p0 >= 1)
+        return 1;
+    const pObs = binomPmf(k, n, p0);
+    let total = 0;
+    const tol = pObs * (1 + 1e-7);
+    for (let j = 0; j <= n; j++) {
+        const pj = binomPmf(j, n, p0);
+        if (pj <= tol)
+            total += pj;
+    }
+    return Math.min(1, total);
+}
+/**
+ * Benjamini-Hochberg FDR adjustment. Given raw p-values, returns the
+ * adjusted q-values in the SAME order as the input. Standard step-up:
+ * sort ascending, q_i = p_i * m / rank, then enforce monotonicity from
+ * the largest rank downward, clamp to [0, 1].
+ */
+function benjaminiHochberg(pvalues) {
+    const m = pvalues.length;
+    if (m === 0)
+        return [];
+    const indexed = pvalues.map((p, i) => ({ p, i })).sort((a, b) => a.p - b.p);
+    const q = new Array(m);
+    let prev = 1;
+    for (let rank = m; rank >= 1; rank--) {
+        const { p, i } = indexed[rank - 1];
+        const raw = (p * m) / rank;
+        prev = Math.min(prev, raw);
+        q[i] = Math.min(1, prev);
+    }
+    return q;
+}
+// ─── Per-token statistics ─────────────────────────────────────────────────
+/**
+ * Compute per-token verdict statistics with the full significance floor.
+ * Only tokens appearing in >= minOccurrences plans are TESTED (and thus
+ * counted in the multiple-comparison correction). A tested token is
+ * `significant` iff effect_size >= effectSize AND raw_p < 0.05 AND
+ * fdr_q < fdrQ.
+ *
+ * STATISTICAL CAVEAT (codex review P2): the null rate is the observed global
+ * baseline, which INCLUDES the token's own rows. The token and the baseline
+ * are therefore not independent, so `raw_p` / `fdr_q` are an *approximate
+ * association signal*, NOT exactly calibrated p-values. This is deliberate
+ * and acceptable for a suggest-to-a-human heuristic miner — the floor exists
+ * to rank and gate noise, not to publish inference. A properly independent
+ * test (two-sample / Fisher exact: token-rows vs non-token-rows) is a v0.5
+ * follow-up if these suggestions ever feed an automated decision. They do
+ * not: every suggestion is human-reviewed before promotion.
+ */
+function computeTokenStats(reflections, opts) {
+    const total = reflections.length;
+    if (total === 0)
+        return { baseline: 0, stats: [] };
+    const confirmedTotal = reflections.filter((r) => r.confirmed).length;
+    const baseline = confirmedTotal / total;
+    // Tally per token.
+    const counts = new Map();
+    for (const r of reflections) {
+        for (const tok of r.vocabulary) {
+            const c = counts.get(tok) ?? { n: 0, confirmed: 0 };
+            c.n += 1;
+            if (r.confirmed)
+                c.confirmed += 1;
+            counts.set(tok, c);
+        }
+    }
+    // Only tokens meeting the occurrence floor are tested (drives FDR m).
+    const tested = [];
+    for (const [token, c] of counts) {
+        if (c.n < opts.minOccurrences)
+            continue;
+        const raw_p = binomTwoSidedP(c.confirmed, c.n, baseline);
+        tested.push({ token, n: c.n, confirmed: c.confirmed, raw_p });
+    }
+    const qvals = benjaminiHochberg(tested.map((t) => t.raw_p));
+    const stats = tested.map((t, idx) => {
+        const confirmed_rate = t.confirmed / t.n;
+        const effect_size = Math.abs(confirmed_rate - baseline);
+        const fdr_q = qvals[idx];
+        const significant = effect_size >= opts.effectSize && t.raw_p < 0.05 && fdr_q < opts.fdrQ;
+        return {
+            token: t.token,
+            n: t.n,
+            confirmed: t.confirmed,
+            confirmed_rate,
+            baseline,
+            effect_size,
+            raw_p: t.raw_p,
+            fdr_q,
+            significant,
+        };
+    });
+    // Deterministic ordering: significant first, then by effect size desc,
+    // then token asc for stable output.
+    stats.sort((a, b) => {
+        if (a.significant !== b.significant)
+            return a.significant ? -1 : 1;
+        if (b.effect_size !== a.effect_size)
+            return b.effect_size - a.effect_size;
+        return a.token < b.token ? -1 : a.token > b.token ? 1 : 0;
+    });
+    return { baseline, stats };
+}
+// ─── Suggestion formatting ──────────────────────────────────────────────────
+function formatSuggestionsBlock(suggestions, baseline) {
+    const date = new Date().toISOString().slice(0, 10);
+    const lines = [`## Run ${date}`, ''];
+    for (const s of suggestions) {
+        const dir = s.confirmed_rate >= baseline ? 'more' : 'less';
+        const sign = s.confirmed_rate >= baseline ? '+' : '-';
+        lines.push(`- Plans containing "${s.token}" have ${(s.confirmed_rate * 100).toFixed(0)}% confirmed ` +
+            `(baseline ${(baseline * 100).toFixed(0)}%, n=${s.n}, raw_p=${s.raw_p.toFixed(4)}, ` +
+            `fdr_q=${s.fdr_q.toFixed(4)}, effect_size=${sign}${s.effect_size.toFixed(2)}).`);
+        lines.push(`  Suggested heuristic: "Plans involving \`${s.token}\` succeed ${dir} often than baseline."`);
+        lines.push(`  Promote with: \`gd genome promote-suggestion ${s.token}-rate\``);
+        lines.push('');
+    }
+    return lines.join('\n');
+}
+// ─── CLI entry ─────────────────────────────────────────────────────────────
+function cmdPatterns(cwd, opts, raw) {
+    const minOccurrences = opts.minOccurrences ?? 10;
+    const effectSize = opts.effectSize ?? 0.2;
+    const fdrQ = opts.fdrQ ?? 0.1;
+    const reflections = scanReflections(cwd);
+    const { baseline, stats } = computeTokenStats(reflections, {
+        minOccurrences,
+        effectSize,
+        fdrQ,
+    });
+    const suggestions = stats.filter((s) => s.significant);
+    let applied = false;
+    let suggestionsPath = null;
+    if (opts.apply) {
+        // never-auto-write: --apply requires explicit --yes confirmation.
+        if (!opts.yes) {
+            error('--apply requires --yes (writes to .planning/GENOME-SUGGESTIONS.md). Refusing.');
+        }
+        suggestionsPath = path.join(cwd, '.planning', 'GENOME-SUGGESTIONS.md');
+        if (suggestions.length > 0) {
+            const header = fileExists(suggestionsPath)
+                ? safeReadMarkdown(suggestionsPath) ?? ''
+                : '# GENOME suggestions (auto-generated — NOT read by the planner)\n\n' +
+                    'Deterministic pattern-extractor output. Promote an entry into the\n' +
+                    'prescriptive GENOME.md only via `gd genome promote-suggestion <slug>`\n' +
+                    '(human-curated). The planner reads GENOME.md ONLY.\n\n';
+            const block = formatSuggestionsBlock(suggestions, baseline);
+            atomicWriteFileSync(suggestionsPath, `${header}${block}\n`);
+            applied = true;
+        }
+    }
+    const result = {
+        reflections_scanned: reflections.length,
+        baseline_confirmed_rate: baseline,
+        tokens_tested: stats.length,
+        suggestions,
+        applied,
+        suggestions_path: applied ? path.relative(cwd, suggestionsPath) : null,
+    };
+    const rawSummary = suggestions.length === 0
+        ? `no significant patterns (${reflections.length} reflections, ${stats.length} tokens tested)`
+        : `${suggestions.length} suggestion(s) from ${reflections.length} reflections` +
+            (applied ? ` → written to ${result.suggestions_path}` : ' (dry-run; --apply --yes to write)') +
+            '\n' +
+            formatSuggestionsBlock(suggestions, baseline);
+    output(result, raw, rawSummary);
+}
+module.exports = {
+    isConfirmed,
+    scanReflections,
+    binomTwoSidedP,
+    benjaminiHochberg,
+    computeTokenStats,
+    cmdPatterns,
+};
+//# sourceMappingURL=patterns.js.map

package/dist/lib/commands/patterns.js.map

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package/dist/lib/commands/phase-info.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=phase-info.d.ts.map

package/dist/lib/commands/phase-info.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"phase-info.d.ts","sourceRoot":"","sources":["../../../lib/commands/phase-info.ts"],"names":[],"mappings":""}