@jokerized/getresearchdone 0.4.1

package/dist/lib/gates.js

@@ -0,0 +1,578 @@
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+const fs = require('fs');
+const path = require('path');
+const { loadConfig, normalizePhaseName, safeReadFile, stripShippedSections, createRunCache, } = require('./utils');
+const { phasesDir: getPhasesDirPath } = require('./paths');
+const { validateStructural, validateCrossPhase, extractPlanArtifact } = require('./invariants');
+const { buildCitationGraph, findUnresolved } = require('./citations');
+// ─── File Content Cache ───────────────────────────────────────────────────────
+const _gatesCache = createRunCache();
+function _gatesCachedRead(p) {
+    return _gatesCache.get(p, safeReadFile);
+}
+// ─── Gate Check Functions ─────────────────────────────────────────────────────
+/**
+ * Check for phase directories on disk that are not in ROADMAP.md.
+ */
+function checkOrphanedPhases(cwd) {
+    const violations = [];
+    const roadmapPath = path.join(cwd, '.planning', 'ROADMAP.md');
+    const phasesDir = getPhasesDirPath(cwd);
+    const roadmapContent = _gatesCachedRead(roadmapPath);
+    if (!roadmapContent)
+        return violations;
+    const activeContent = stripShippedSections(roadmapContent);
+    // Extract phases from ROADMAP
+    const roadmapPhases = new Set();
+    const phasePattern = /#{2,3}\s*Phase\s+(\d+(?:\.\d+)?)\s*:/gi;
+    let m;
+    while ((m = phasePattern.exec(activeContent)) !== null) {
+        roadmapPhases.add(m[1]);
+    }
+    // Get phases on disk
+    try {
+        const entries = fs.readdirSync(phasesDir, {
+            withFileTypes: true,
+        });
+        const dirs = entries
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name);
+        for (const dir of dirs) {
+            const dm = dir.match(/^(\d+(?:\.\d+)?)/);
+            if (!dm)
+                continue;
+            const phaseNum = dm[1];
+            const unpadded = String(parseInt(phaseNum, 10));
+            if (!roadmapPhases.has(phaseNum) && !roadmapPhases.has(unpadded)) {
+                violations.push({
+                    code: 'ORPHANED_PHASE',
+                    severity: 'error',
+                    message: `Phase directory "${dir}" exists on disk but not in ROADMAP.md`,
+                    fix: 'Run `/grd:complete-milestone` to archive old phase directories, or manually remove the orphaned directory',
+                    context: { directory: dir, phase_number: phaseNum },
+                });
+            }
+        }
+    }
+    catch (err) {
+        // ENOENT: phases dir may not exist — silent
+        const fsErr = err;
+        if (fsErr.code !== 'ENOENT') {
+            process.stderr.write(`Warning: unexpected error reading phases directory: ${fsErr.message}\n`);
+        }
+    }
+    return violations;
+}
+/**
+ * Check that a target phase exists in ROADMAP.md.
+ */
+function checkPhaseInRoadmap(cwd, phase) {
+    const violations = [];
+    if (!phase)
+        return violations;
+    const roadmapPath = path.join(cwd, '.planning', 'ROADMAP.md');
+    const phasesDir = getPhasesDirPath(cwd);
+    const roadmapContent = _gatesCachedRead(roadmapPath);
+    if (!roadmapContent)
+        return violations;
+    const activeContent = stripShippedSections(roadmapContent);
+    // Only flag if the phase exists on disk but not in ROADMAP.
+    // If it doesn't exist on disk either, let normal command logic handle "not found".
+    const normalized = normalizePhaseName(phase);
+    let existsOnDisk = false;
+    try {
+        const entries = fs.readdirSync(phasesDir, {
+            withFileTypes: true,
+        });
+        const dirs = entries
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name);
+        existsOnDisk = dirs.some((d) => d.startsWith(normalized));
+    }
+    catch {
+        // phases dir may not exist
+    }
+    if (!existsOnDisk)
+        return violations;
+    const unpadded = String(parseInt(normalized, 10));
+    const phaseRegex = new RegExp(`#{2,}\\s*Phase\\s+(?:${normalized}|${unpadded})\\s*:`, 'i');
+    if (!phaseRegex.test(activeContent)) {
+        violations.push({
+            code: 'PHASE_NOT_IN_ROADMAP',
+            severity: 'error',
+            message: `Phase ${phase} not found in ROADMAP.md — may be from a previous milestone`,
+            fix: 'Ensure the phase exists in the current ROADMAP.md, or archive old phases with `/grd:complete-milestone`',
+            context: { phase },
+        });
+    }
+    return violations;
+}
+/**
+ * Check that a target phase has at least one plan.
+ */
+function checkPhaseHasPlans(cwd, phase) {
+    const violations = [];
+    if (!phase)
+        return violations;
+    const phasesDir = getPhasesDirPath(cwd);
+    const normalized = normalizePhaseName(phase);
+    try {
+        const entries = fs.readdirSync(phasesDir, {
+            withFileTypes: true,
+        });
+        const dirs = entries
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name);
+        const match = dirs.find((d) => d.startsWith(normalized));
+        if (!match)
+            return violations;
+        const phaseFiles = fs.readdirSync(path.join(phasesDir, match));
+        const plans = phaseFiles.filter((f) => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+        if (plans.length === 0) {
+            violations.push({
+                code: 'PHASE_NO_PLANS',
+                severity: 'error',
+                message: `Phase ${phase} has no plans — run /grd:plan-phase ${phase} first`,
+                fix: `Run \`/grd:plan-phase ${phase}\` to create execution plans`,
+                context: { phase, directory: match },
+            });
+        }
+    }
+    catch {
+        // phase dir may not exist
+    }
+    return violations;
+}
+/**
+ * Check for stale artifacts (summaries without matching plans).
+ */
+function checkNoStaleArtifacts(cwd, phase) {
+    const violations = [];
+    if (!phase)
+        return violations;
+    const phasesDir = getPhasesDirPath(cwd);
+    const normalized = normalizePhaseName(phase);
+    try {
+        const entries = fs.readdirSync(phasesDir, {
+            withFileTypes: true,
+        });
+        const dirs = entries
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name);
+        const match = dirs.find((d) => d.startsWith(normalized));
+        if (!match)
+            return violations;
+        const phaseFiles = fs.readdirSync(path.join(phasesDir, match));
+        const plans = new Set(phaseFiles
+            .filter((f) => f.endsWith('-PLAN.md'))
+            .map((f) => f.replace('-PLAN.md', '')));
+        const summaries = phaseFiles
+            .filter((f) => f.endsWith('-SUMMARY.md'))
+            .map((f) => f.replace('-SUMMARY.md', ''));
+        for (const sid of summaries) {
+            if (!plans.has(sid)) {
+                violations.push({
+                    code: 'STALE_ARTIFACTS',
+                    severity: 'warning',
+                    message: `Summary ${sid}-SUMMARY.md in phase ${phase} has no matching PLAN.md`,
+                    fix: 'Remove the orphaned summary or recreate the missing plan',
+                    context: { phase, summary: `${sid}-SUMMARY.md` },
+                });
+            }
+        }
+    }
+    catch {
+        // phase dir may not exist
+    }
+    return violations;
+}
+/**
+ * Check that completed milestone phases have been archived.
+ */
+function checkOldPhasesArchived(cwd) {
+    const violations = [];
+    const statePath = path.join(cwd, '.planning', 'STATE.md');
+    const phasesDir = getPhasesDirPath(cwd);
+    const stateContent = safeReadFile(statePath);
+    if (!stateContent)
+        return violations;
+    // Check if STATE.md indicates a milestone was completed
+    const milestoneCompletePattern = /milestone\s+complete/i;
+    if (!milestoneCompletePattern.test(stateContent))
+        return violations;
+    // If milestone is marked complete, phases dir should be empty
+    try {
+        const entries = fs.readdirSync(phasesDir, {
+            withFileTypes: true,
+        });
+        const dirs = entries
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name);
+        if (dirs.length > 0) {
+            violations.push({
+                code: 'UNARCHIVED_PHASES',
+                severity: 'error',
+                message: `STATE.md indicates milestone complete but ${dirs.length} phase directories remain on disk`,
+                fix: 'Run `/grd:complete-milestone` to properly archive phase directories before starting a new milestone',
+                context: { phase_count: dirs.length, directories: dirs },
+            });
+        }
+    }
+    catch {
+        // phases dir may not exist
+    }
+    return violations;
+}
+/**
+ * Check milestone state coherence between STATE.md and disk state.
+ */
+function checkMilestoneStateCoherence(cwd) {
+    const violations = [];
+    const statePath = path.join(cwd, '.planning', 'STATE.md');
+    const roadmapPath = path.join(cwd, '.planning', 'ROADMAP.md');
+    const stateContent = safeReadFile(statePath);
+    if (!stateContent)
+        return violations;
+    const roadmapContent = _gatesCachedRead(roadmapPath);
+    const activeContent = roadmapContent ? stripShippedSections(roadmapContent) : null;
+    // Check: STATE references a phase that doesn't exist in ROADMAP
+    const activePhaseMatch = stateContent.match(/\*\*(?:Active phase|Current Phase):\*\*\s*(\d+(?:\.\d+)?)/i);
+    if (activePhaseMatch && activeContent) {
+        const activePhase = activePhaseMatch[1];
+        const unpadded = String(parseInt(activePhase, 10));
+        const phaseInRoadmap = new RegExp(`#{2,}\\s*Phase\\s+(?:${activePhase}|${unpadded})\\s*:`, 'i');
+        if (!phaseInRoadmap.test(activeContent)) {
+            violations.push({
+                code: 'MILESTONE_STATE_CONFUSION',
+                severity: 'error',
+                message: `STATE.md references Phase ${activePhase} but it does not exist in ROADMAP.md`,
+                fix: 'Update STATE.md to reference a valid phase, or run `/grd:complete-milestone` to reset state',
+                context: { active_phase: activePhase },
+            });
+        }
+    }
+    return violations;
+}
+/**
+ * Check plan invariants: structural validity for each plan and cross-phase consistency.
+ *
+ * Satisfies REQ-180 (Pre-Flight Validation Gate): invalid plans are hard-rejected
+ * before execution. Reads all *-PLAN.md files in the target phase directory,
+ * runs validateStructural per plan, then validateCrossPhase across all plans.
+ */
+function checkInvariantValidation(cwd, opts) {
+    const violations = [];
+    if (!opts.phase)
+        return violations;
+    const phasesDir = getPhasesDirPath(cwd);
+    const normalized = normalizePhaseName(opts.phase);
+    // Locate the phase directory on disk
+    let phaseDir;
+    try {
+        const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+        const match = entries
+            .filter((e) => e.isDirectory())
+            .map((e) => e.name)
+            .find((d) => d.startsWith(normalized));
+        if (!match)
+            return violations;
+        phaseDir = path.join(phasesDir, match);
+    }
+    catch {
+        return violations;
+    }
+    // Read all *-PLAN.md files
+    let planFiles;
+    try {
+        const phaseContents = fs.readdirSync(phaseDir);
+        planFiles = phaseContents.filter((f) => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+    }
+    catch {
+        return violations;
+    }
+    if (planFiles.length === 0)
+        return violations;
+    const planArtifacts = [];
+    // Structural validation per plan
+    for (const planFile of planFiles) {
+        const planPath = path.join(phaseDir, planFile);
+        const content = safeReadFile(planPath);
+        if (!content)
+            continue;
+        const artifact = extractPlanArtifact(content);
+        planArtifacts.push(artifact);
+        const result = validateStructural(artifact);
+        for (const err of result.errors) {
+            violations.push({
+                code: 'INVARIANT_STRUCTURAL',
+                severity: 'error',
+                message: `${planFile}: ${err}`,
+                fix: `Fix the structural issue in ${planFile} before execution`,
+                context: { plan: planFile, error: err },
+            });
+        }
+        for (const warn of result.warnings) {
+            violations.push({
+                code: 'INVARIANT_STRUCTURAL',
+                severity: 'warning',
+                message: `${planFile}: ${warn}`,
+                fix: `Consider fixing the structural warning in ${planFile}`,
+                context: { plan: planFile, warning: warn },
+            });
+        }
+    }
+    // Cross-phase validation across all plans in the set
+    if (planArtifacts.length > 0) {
+        const crossResult = validateCrossPhase(planArtifacts);
+        for (const err of crossResult.errors) {
+            violations.push({
+                code: 'INVARIANT_CROSS_PHASE',
+                severity: 'error',
+                message: err,
+                fix: 'Resolve cross-phase dependency conflicts between plans',
+                context: { error: err },
+            });
+        }
+        for (const warn of crossResult.warnings) {
+            violations.push({
+                code: 'INVARIANT_CROSS_PHASE',
+                severity: 'warning',
+                message: warn,
+                fix: 'Consider adding provides/requires to plans for dependency tracking',
+                context: { warning: warn },
+            });
+        }
+    }
+    return violations;
+}
+/**
+ * Check for unresolved critical citation dependencies.
+ *
+ * Only runs when citation_gate is enabled in config (default: false).
+ * Reads the citation graph from .planning/research/PAPERS.md if it exists.
+ * Returns GateViolation[] for each critical unresolved CitationNode.
+ *
+ * Satisfies REQ-184 (Citation Recovery — configurable gate).
+ */
+function checkCitationGate(cwd, _opts) {
+    const violations = [];
+    const config = loadConfig(cwd);
+    // Only run if citation_gate is enabled in config (default: false)
+    const citationGateEnabled = config.citation_gate === true;
+    if (!citationGateEnabled)
+        return violations;
+    // Find research directory for current milestone
+    const researchDir = path.join(cwd, '.planning', 'research');
+    const papersPath = path.join(researchDir, 'PAPERS.md');
+    // Only check if PAPERS.md exists
+    try {
+        fs.statSync(papersPath);
+    }
+    catch {
+        return violations;
+    }
+    try {
+        const graph = buildCitationGraph(researchDir);
+        const criticalUnresolved = findUnresolved(graph, 'critical');
+        for (const node of criticalUnresolved) {
+            violations.push({
+                code: 'CITATION_UNRESOLVED_CRITICAL',
+                severity: 'error',
+                message: `Critical citation dependency "${node.slug}" (${node.title}) is unresolved — run citation recovery before planning`,
+                fix: 'Run `/grd:research-phase` with citation recovery enabled, or manually resolve the dependency',
+                context: { slug: node.slug, title: node.title, priority: node.priority },
+            });
+        }
+    }
+    catch {
+        // Citation graph build failed — non-blocking
+    }
+    return violations;
+}
+/**
+ * Check for unresolved transitive citation dependencies (warning severity).
+ *
+ * Only runs when transitive_citation_gate is enabled in config (default: false).
+ * Performs BFS traversal of the citation graph and reports unresolved leaf nodes
+ * as warnings — these do not block plan-phase execution.
+ *
+ * Warning (not error) severity follows the principle that transitive dependencies
+ * are informational — they inform what additional work may be needed without
+ * blocking a researcher from planning a phase.
+ */
+function checkTransitiveCitationGate(cwd, _opts) {
+    const violations = [];
+    const config = loadConfig(cwd);
+    const enabled = config.transitive_citation_gate === true;
+    if (!enabled)
+        return violations;
+    const researchDir = path.join(cwd, '.planning', 'research');
+    const papersPath = path.join(researchDir, 'PAPERS.md');
+    try {
+        fs.statSync(papersPath);
+    }
+    catch {
+        return violations;
+    }
+    try {
+        const graph = buildCitationGraph(researchDir);
+        const { traverseCitationGraph } = require('./citations');
+        const result = traverseCitationGraph(graph);
+        for (const node of result.unresolved_leaves) {
+            violations.push({
+                code: 'CITATION_UNRESOLVED_TRANSITIVE',
+                severity: 'warning',
+                message: `Transitive citation dependency "${node.slug}" is unresolved — consider running auto-retrieval`,
+                fix: 'Enable transitive auto-retrieval or manually add a PAPERS.md entry for this dependency',
+                context: { slug: node.slug, priority: node.priority },
+            });
+        }
+    }
+    catch {
+        // Non-blocking
+    }
+    return violations;
+}
+// ─── Gate Registry ────────────────────────────────────────────────────────────
+/**
+ * Declarative mapping of commands to their required gate checks.
+ */
+const GATE_REGISTRY = {
+    'execute-phase': [
+        'orphaned-phases',
+        'phase-in-roadmap',
+        'phase-has-plans',
+        'invariant-validation',
+    ],
+    'plan-phase': [
+        'orphaned-phases',
+        'phase-in-roadmap',
+        'no-stale-artifacts',
+        'invariant-validation',
+        'citation-gate',
+        'transitive-citation-gate',
+    ],
+    'new-milestone': ['old-phases-archived', 'milestone-state-coherence'],
+    'phase-add': ['orphaned-phases'],
+    'phase-insert': ['orphaned-phases'],
+    'phase-complete': ['phase-in-roadmap'],
+    'milestone-complete': ['milestone-state-coherence'],
+    'verify-work': ['phase-in-roadmap'],
+    iterate: ['phase-in-roadmap', 'phase-has-plans'],
+};
+/**
+ * Map gate names to check functions.
+ */
+const GATE_CHECKS = {
+    'orphaned-phases': (cwd) => checkOrphanedPhases(cwd),
+    'phase-in-roadmap': (cwd, opts) => checkPhaseInRoadmap(cwd, opts.phase || ''),
+    'phase-has-plans': (cwd, opts) => checkPhaseHasPlans(cwd, opts.phase || ''),
+    'no-stale-artifacts': (cwd, opts) => checkNoStaleArtifacts(cwd, opts.phase || ''),
+    'old-phases-archived': (cwd) => checkOldPhasesArchived(cwd),
+    'milestone-state-coherence': (cwd) => checkMilestoneStateCoherence(cwd),
+    'invariant-validation': (cwd, opts) => checkInvariantValidation(cwd, opts),
+    'citation-gate': (cwd, opts) => checkCitationGate(cwd, opts),
+    'transitive-citation-gate': (cwd, opts) => checkTransitiveCitationGate(cwd, opts),
+};
+// ─── Main Entry Point ─────────────────────────────────────────────────────────
+/**
+ * Run pre-flight gate checks for a command.
+ */
+function runPreflightGates(cwd, command, options = {}) {
+    const result = {
+        passed: true,
+        bypassed: false,
+        errors: [],
+        warnings: [],
+        command,
+    };
+    // skipGates: true bypasses all checks immediately
+    if (options.skipGates) {
+        result.bypassed = true;
+        return result;
+    }
+    // New project safety: if no ROADMAP.md exists, all checks pass
+    const roadmapPath = path.join(cwd, '.planning', 'ROADMAP.md');
+    try {
+        fs.statSync(roadmapPath);
+    }
+    catch {
+        return result;
+    }
+    // Look up gates for this command
+    const gateNames = GATE_REGISTRY[command];
+    if (!gateNames)
+        return result;
+    _gatesCache.init();
+    try {
+        // Run each gate check
+        for (const gateName of gateNames) {
+            const checkFn = GATE_CHECKS[gateName];
+            if (!checkFn)
+                continue;
+            try {
+                const violations = checkFn(cwd, options);
+                for (const v of violations) {
+                    if (v.severity === 'error') {
+                        result.errors.push(v);
+                    }
+                    else {
+                        result.warnings.push(v);
+                    }
+                }
+            }
+            catch (e) {
+                const msg = e.message || String(e);
+                process.stderr.write(`[gates] gate '${gateName}' threw: ${msg}\n`);
+                result.warnings.push({
+                    code: 'GATE_ERROR',
+                    severity: 'warning',
+                    message: `Gate '${gateName}' internal error: ${msg}`,
+                    fix: 'Check the gate implementation for bugs or update the failing check',
+                    context: {},
+                });
+            }
+        }
+        // YOLO bypass: if autonomous_mode is enabled, pass regardless of errors
+        const config = loadConfig(cwd);
+        if (config.autonomous_mode) {
+            result.bypassed = true;
+            result.passed = true;
+            return result;
+        }
+        // Determine pass/fail based on errors
+        if (result.errors.length > 0) {
+            result.passed = false;
+        }
+        return result;
+    }
+    finally {
+        _gatesCache.reset();
+    }
+}
+/**
+ * Reset the internal gates run cache (useful for testing).
+ */
+function resetGatesCache() {
+    _gatesCache.reset();
+}
+// ─── Exports ──────────────────────────────────────────────────────────────────
+module.exports = {
+    // Gate check functions (for direct use and testing)
+    checkOrphanedPhases,
+    checkPhaseInRoadmap,
+    checkPhaseHasPlans,
+    checkNoStaleArtifacts,
+    checkOldPhasesArchived,
+    checkMilestoneStateCoherence,
+    checkInvariantValidation,
+    checkCitationGate,
+    checkTransitiveCitationGate,
+    // Registry and runner
+    GATE_REGISTRY,
+    _GATE_CHECKS: GATE_CHECKS,
+    runPreflightGates,
+    resetGatesCache,
+};
+//# sourceMappingURL=gates.js.map

package/dist/lib/gates.js.map

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

@@ -0,0 +1,10 @@
+export interface SnapshotResult {
+    action: 'created' | 'appended';
+    snapshot_date: string;
+    path: string;
+}
+/** Sentinel error thrown by runGenomeSnapshot when GENOME.md is split-index. */
+export declare class GenomeSplitIndexError extends Error {
+    constructor(message: string);
+}
+//# sourceMappingURL=genome.d.ts.map

package/dist/lib/genome.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"genome.d.ts","sourceRoot":"","sources":["../../lib/genome.ts"],"names":[],"mappings":"AAuPA,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,SAAS,GAAG,UAAU,CAAC;IAC/B,aAAa,EAAE,MAAM,CAAC;IACtB,IAAI,EAAE,MAAM,CAAC;CACd;AAED,gFAAgF;AAChF,qBAAa,qBAAsB,SAAQ,KAAK;gBAClC,OAAO,EAAE,MAAM;CAI5B"}