@jokerized/getresearchdone 0.4.1

package/dist/lib/commands/knowledge-search.js

@@ -0,0 +1,113 @@
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+/** GRD Commands/KnowhowSearch -- Keyword search across all milestone KNOWHOW.md files */
+const fs = require('fs');
+const path = require('path');
+const { output, error, } = require('../utils');
+const { parseKnowhowEntries, } = require('../knowledge');
+function _tokenize(text) {
+    return text.toLowerCase().split(/\W+/).filter((t) => t.length > 1);
+}
+function _score(entry, queryTokens) {
+    const haystack = [entry.pattern_name, entry.applicability, entry.source, entry.code_snippet]
+        .join(' ')
+        .toLowerCase();
+    let score = 0;
+    for (const token of queryTokens) {
+        if (haystack.includes(token))
+            score += 1;
+        // Bonus for exact match in pattern name
+        if (entry.pattern_name.toLowerCase().includes(token))
+            score += 1;
+    }
+    return score;
+}
+/**
+ * CLI command: Search all KNOWHOW.md files across milestones for entries matching query.
+ */
+function cmdKnowhowSearch(cwd, query, topN, raw) {
+    if (!query || !query.trim()) {
+        error('query required. Usage: gd knowledge search <query> [--top N]');
+    }
+    const milestonesBase = path.join(cwd, '.planning', 'milestones');
+    if (!fs.existsSync(milestonesBase)) {
+        output({ query, total_searched: 0, hits: 0, results: [] }, raw, '0');
+        return;
+    }
+    const queryTokens = _tokenize(query);
+    const hits = [];
+    let totalSearched = 0;
+    let msDirs;
+    try {
+        msDirs = fs
+            .readdirSync(milestonesBase, { withFileTypes: true })
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name);
+    }
+    catch {
+        msDirs = [];
+    }
+    // Codex r18 P2: KNOWHOW entries live in three places per milestone —
+    // top-level KNOWHOW.md, the research/ subdir, and per-phase dirs.
+    // Scan all three so cross-milestone search finds real entries.
+    for (const ms of msDirs) {
+        const msPaths = [
+            path.join(milestonesBase, ms, 'KNOWHOW.md'),
+            path.join(milestonesBase, ms, 'research', 'KNOWHOW.md'),
+        ];
+        try {
+            const phasesBase = path.join(milestonesBase, ms, 'phases');
+            for (const ph of fs.readdirSync(phasesBase)) {
+                msPaths.push(path.join(phasesBase, ph, 'KNOWHOW.md'));
+            }
+        }
+        catch { /* no phases dir */ }
+        for (const knowhowPath of msPaths) {
+            let content;
+            try {
+                content = fs.readFileSync(knowhowPath, 'utf-8');
+            }
+            catch {
+                continue;
+            }
+            const entries = parseKnowhowEntries(content);
+            totalSearched += entries.length;
+            for (const entry of entries) {
+                const score = _score(entry, queryTokens);
+                if (score > 0) {
+                    hits.push({
+                        pattern_name: entry.pattern_name,
+                        milestone: ms,
+                        source: entry.source,
+                        applicability: entry.applicability,
+                        code_snippet: entry.code_snippet,
+                        phase_number: entry.phase_number,
+                        created_at: entry.created_at,
+                        score,
+                    });
+                }
+            }
+        }
+    }
+    hits.sort((a, b) => b.score - a.score || b.phase_number - a.phase_number);
+    const results = hits.slice(0, topN > 0 ? topN : 10);
+    const result = {
+        query,
+        total_searched: totalSearched,
+        hits: hits.length,
+        results,
+    };
+    if (raw) {
+        const lines = [`Knowledge search: "${query}" — ${hits.length} hit(s) of ${totalSearched} entries`];
+        for (const r of results) {
+            lines.push(`[${r.milestone}/phase ${r.phase_number}] ${r.pattern_name} (score: ${r.score})`);
+            lines.push(`  ${r.applicability}`);
+        }
+        output(result, raw, lines.join('\n'));
+    }
+    else {
+        output(result, raw, `${hits.length} hits`);
+    }
+}
+module.exports = { cmdKnowhowSearch };
+//# sourceMappingURL=knowledge-search.js.map

package/dist/lib/commands/knowledge-search.js.map

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package/dist/lib/commands/long-term-roadmap.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=long-term-roadmap.d.ts.map

package/dist/lib/commands/long-term-roadmap.d.ts.map

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

package/dist/lib/commands/long-term-roadmap.js

@@ -0,0 +1,272 @@
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+/** GRD Commands/LongTermRoadmap -- Long-term roadmap CRUD operations CLI interface */
+const path = require('path');
+const { safeReadFile, output, error, } = require('../utils');
+const { planningDir: getPlanningDir, } = require('../paths');
+const { parseLongTermRoadmap, validateLongTermRoadmap, formatLongTermRoadmap, updateRefinementHistory, addLtMilestone, removeLtMilestone, updateLtMilestone, linkNormalMilestone, unlinkNormalMilestone, getLtMilestoneById, initFromRoadmap, } = require('../long-term-roadmap');
+const { readCachedRoadmap, } = require('./phase-info');
+// ─── Helpers ─────────────────────────────────────────────────────────────────
+/** Extract --flag value from args array, returns value or fallback. */
+function flag(args, name, fallback) {
+    const i = args.indexOf(name);
+    return i !== -1 && i + 1 < args.length ? args[i + 1] : (fallback ?? null);
+}
+/** Compute relative path to LONG-TERM-ROADMAP.md from cwd. */
+function ltrmRelPath(cwd) {
+    return path.relative(cwd, path.join(getPlanningDir(cwd), 'LONG-TERM-ROADMAP.md'));
+}
+// ─── Long-Term Roadmap Command ──────────────────────────────────────────────
+/**
+ * CLI command: Manage long-term roadmap operations.
+ *
+ * Delegates to the corresponding function in lib/long-term-roadmap.ts for each subcommand.
+ * Supports: list, add, remove, update, refine, link, unlink, display, init, history, parse, validate.
+ *
+ * @param cwd - Project working directory
+ * @param subcommand - Operation to perform
+ * @param args - Remaining CLI arguments (flags and values)
+ * @param raw - Output raw text instead of JSON
+ */
+function cmdLongTermRoadmap(cwd, subcommand, args, raw) {
+    const ltrmPath = path.join(getPlanningDir(cwd), 'LONG-TERM-ROADMAP.md');
+    const roadmapPath = path.join(getPlanningDir(cwd), 'ROADMAP.md');
+    function readLtrm() {
+        const content = safeReadFile(ltrmPath);
+        if (!content) {
+            output({ error: 'LONG-TERM-ROADMAP.md not found', exists: false }, raw, '');
+            return null;
+        }
+        return content;
+    }
+    switch (subcommand) {
+        // List all LT milestones with ID, name, and status
+        case 'list': {
+            const content = readLtrm();
+            if (!content)
+                return;
+            const parsed = parseLongTermRoadmap(content);
+            const milestones = parsed ? parsed.milestones : [];
+            const summary = milestones.map((m) => `${m.id}: ${m.name} [${m.status}]`).join('\n');
+            output({ milestones, count: milestones.length }, raw, summary || '(no milestones)');
+            break;
+        }
+        // Add a new LT milestone with --name and --goal
+        case 'add': {
+            const name = flag(args, '--name');
+            const goal = flag(args, '--goal');
+            if (!name) {
+                error('--name flag required');
+                return;
+            }
+            if (!goal) {
+                error('--goal flag required');
+                return;
+            }
+            const content = readLtrm();
+            if (!content)
+                return;
+            const result = addLtMilestone(content, name, goal);
+            output({ content: result.content, path: ltrmRelPath(cwd), id: result.id }, raw, result.content);
+            break;
+        }
+        // Remove an LT milestone by --id (checks for linked normal milestones)
+        case 'remove': {
+            const id = flag(args, '--id');
+            if (!id) {
+                error('--id flag required');
+                return;
+            }
+            const content = readLtrm();
+            if (!content)
+                return;
+            const roadmapContent = readCachedRoadmap(roadmapPath);
+            const result = removeLtMilestone(content, id, roadmapContent ?? undefined);
+            if (result && typeof result === 'object' && result.error) {
+                output({ error: result.error }, raw, result.error);
+            }
+            else {
+                output({ content: result, path: ltrmRelPath(cwd), removed: id }, raw, result);
+            }
+            break;
+        }
+        case 'update': {
+            const id = flag(args, '--id');
+            if (!id) {
+                error('--id flag required');
+                return;
+            }
+            const updates = {};
+            const nameVal = flag(args, '--name');
+            const goalVal = flag(args, '--goal');
+            const statusVal = flag(args, '--status');
+            if (nameVal)
+                updates.name = nameVal;
+            if (goalVal)
+                updates.goal = goalVal;
+            if (statusVal)
+                updates.status = statusVal;
+            if (Object.keys(updates).length === 0) {
+                error('At least one of --name, --goal, --status required. Example: long-term-roadmap update <id> --name "New Name" --goal "New Goal" --status active');
+                return;
+            }
+            const content = readLtrm();
+            if (!content)
+                return;
+            const result = updateLtMilestone(content, id, updates);
+            if (result && typeof result === 'object' && result.error) {
+                output({ error: result.error }, raw, result.error);
+            }
+            else {
+                output({ content: result, path: ltrmRelPath(cwd), id, updated_fields: Object.keys(updates) }, raw, result);
+            }
+            break;
+        }
+        case 'refine': {
+            const id = flag(args, '--id');
+            if (!id) {
+                error('--id flag required');
+                return;
+            }
+            const content = readLtrm();
+            if (!content)
+                return;
+            const ms = getLtMilestoneById(content, id);
+            if (!ms) {
+                output({ error: `${id} not found` }, raw, `${id} not found`);
+                return;
+            }
+            output({ milestone: ms, context: `Use this context to discuss refinements for ${id}` }, raw, `${ms.id}: ${ms.name}\nStatus: ${ms.status}\nGoal: ${ms.goal}\nNormal milestones: ${ms.normal_milestones.map((m) => m.version).join(', ') || '(none yet)'}`);
+            break;
+        }
+        case 'link': {
+            const id = flag(args, '--id');
+            const version = flag(args, '--version');
+            const note = flag(args, '--note');
+            if (!id) {
+                error('--id flag required');
+                return;
+            }
+            if (!version) {
+                error('--version flag required');
+                return;
+            }
+            const content = readLtrm();
+            if (!content)
+                return;
+            const result = linkNormalMilestone(content, id, version, note);
+            if (result && typeof result === 'object' && result.error) {
+                output({ error: result.error }, raw, result.error);
+            }
+            else {
+                output({ content: result, path: ltrmRelPath(cwd), id, linked: version }, raw, result);
+            }
+            break;
+        }
+        case 'unlink': {
+            const id = flag(args, '--id');
+            const version = flag(args, '--version');
+            if (!id) {
+                error('--id flag required');
+                return;
+            }
+            if (!version) {
+                error('--version flag required');
+                return;
+            }
+            const content = readLtrm();
+            if (!content)
+                return;
+            const roadmapContent = readCachedRoadmap(roadmapPath);
+            const result = unlinkNormalMilestone(content, id, version, roadmapContent ?? undefined);
+            if (result && typeof result === 'object' && result.error) {
+                output({ error: result.error }, raw, result.error);
+            }
+            else {
+                output({ content: result, path: ltrmRelPath(cwd), id, unlinked: version }, raw, result);
+            }
+            break;
+        }
+        case 'display': {
+            const content = readLtrm();
+            if (!content)
+                return;
+            const parsed = parseLongTermRoadmap(content);
+            const formatted = formatLongTermRoadmap(parsed);
+            const milestoneCount = parsed && parsed.milestones ? parsed.milestones.length : 0;
+            output({ formatted, milestone_count: milestoneCount }, raw, formatted);
+            break;
+        }
+        case 'init': {
+            const roadmapContent = readCachedRoadmap(roadmapPath);
+            if (!roadmapContent) {
+                output({ error: 'ROADMAP.md not found' }, raw, 'ROADMAP.md not found');
+                return;
+            }
+            const projectName = flag(args, '--project') || 'Project';
+            const content = initFromRoadmap(roadmapContent, projectName);
+            output({ content, path: ltrmRelPath(cwd) }, raw, content);
+            break;
+        }
+        case 'history': {
+            const histAction = flag(args, '--action');
+            const histDetails = flag(args, '--details');
+            if (!histAction) {
+                error('--action flag required');
+                return;
+            }
+            if (!histDetails) {
+                error('--details flag required');
+                return;
+            }
+            const content = readLtrm();
+            if (!content)
+                return;
+            const histResult = updateRefinementHistory(content, histAction, histDetails);
+            output({ content: histResult, path: ltrmRelPath(cwd), action: histAction, details: histDetails }, raw, histResult);
+            break;
+        }
+        case 'parse': {
+            const filePath = args[0]
+                ? path.isAbsolute(args[0])
+                    ? args[0]
+                    : path.join(cwd, args[0])
+                : ltrmPath;
+            const content = safeReadFile(filePath);
+            if (!content) {
+                output({ error: 'LONG-TERM-ROADMAP.md not found', exists: false }, raw, '');
+                return;
+            }
+            const parsed = parseLongTermRoadmap(content);
+            const count = parsed && parsed.milestones ? parsed.milestones.length : 0;
+            output(parsed, raw, `${count} LT milestones`);
+            break;
+        }
+        case 'validate': {
+            const valFilePath = args[0]
+                ? path.isAbsolute(args[0])
+                    ? args[0]
+                    : path.join(cwd, args[0])
+                : ltrmPath;
+            const valContent = safeReadFile(valFilePath);
+            if (!valContent) {
+                output({ error: 'LONG-TERM-ROADMAP.md not found', exists: false }, raw, '');
+                return;
+            }
+            const valParsed = parseLongTermRoadmap(valContent);
+            const validation = validateLongTermRoadmap(valParsed);
+            const valRawText = validation.valid
+                ? 'valid'
+                : 'invalid: ' + (validation.errors || []).join('; ');
+            output(validation, raw, valRawText);
+            break;
+        }
+        default:
+            error('Unknown subcommand: ' +
+                subcommand +
+                '. Valid: list, add, remove, update, refine, link, unlink, display, init, history, parse, validate');
+    }
+}
+// ─── Exports ─────────────────────────────────────────────────────────────────
+module.exports = { cmdLongTermRoadmap };
+//# sourceMappingURL=long-term-roadmap.js.map

package/dist/lib/commands/long-term-roadmap.js.map

@@ -0,0 +1 @@
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package/dist/lib/commands/patterns.d.ts

@@ -0,0 +1,91 @@
+export interface Reflection {
+    /** Phase directory the reflection came from (for diagnostics). */
+    source: string;
+    /** Raw verdict string as found in the reflection YAML. */
+    verdict: string;
+    /** Binary outcome: true when the verdict confirms the hypothesis. */
+    confirmed: boolean;
+    /** Token vocabulary of the parent PLAN.md. */
+    vocabulary: Set<string>;
+}
+export interface TokenStat {
+    token: string;
+    n: number;
+    confirmed: number;
+    confirmed_rate: number;
+    baseline: number;
+    effect_size: number;
+    raw_p: number;
+    fdr_q: number;
+    significant: boolean;
+}
+export interface PatternsOptions {
+    minOccurrences?: number;
+    effectSize?: number;
+    fdrQ?: number;
+    apply?: boolean;
+    yes?: boolean;
+}
+export interface PatternsResult {
+    reflections_scanned: number;
+    baseline_confirmed_rate: number;
+    tokens_tested: number;
+    suggestions: TokenStat[];
+    applied: boolean;
+    suggestions_path: string | null;
+}
+/**
+ * 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.
+ */
+export declare function isConfirmed(verdict: string): boolean;
+/**
+ * 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.
+ */
+export declare function scanReflections(cwd: string): Reflection[];
+/**
+ * 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).
+ */
+export declare function binomTwoSidedP(k: number, n: number, p0: number): number;
+/**
+ * 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].
+ */
+export declare function benjaminiHochberg(pvalues: number[]): number[];
+/**
+ * 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.
+ */
+export declare function computeTokenStats(reflections: Reflection[], opts: {
+    minOccurrences: number;
+    effectSize: number;
+    fdrQ: number;
+}): {
+    baseline: number;
+    stats: TokenStat[];
+};
+export declare function cmdPatterns(cwd: string, opts: PatternsOptions, raw: boolean): void;
+//# sourceMappingURL=patterns.d.ts.map

package/dist/lib/commands/patterns.d.ts.map

@@ -0,0 +1 @@
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