@jokerized/getresearchdone 0.4.1

package/dist/lib/scaffold.js

@@ -0,0 +1,355 @@
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+const fs = require('fs');
+const path = require('path');
+const { findPhaseInternal, normalizePhaseName, generateSlugInternal, output, error, } = require('./utils');
+const { reconstructFrontmatter, } = require('./frontmatter');
+const { planningDir: getPlanningDir, phasesDir: getPhasesDirPath, researchDir: getResearchDirPath, } = require('./paths');
+// ─── Template Select ────────────────────────────────────────────────────────
+/**
+ * CLI command: Select the appropriate summary template type based on plan complexity heuristics.
+ * @param cwd - Project working directory
+ * @param planPath - Relative path to the plan file to analyze
+ * @param raw - Output raw template path instead of JSON
+ */
+function cmdTemplateSelect(cwd, planPath, raw) {
+    if (!planPath) {
+        error('plan-path required');
+    }
+    try {
+        const fullPath = path.join(cwd, planPath);
+        const content = fs.readFileSync(fullPath, 'utf-8');
+        // Simple heuristics
+        const taskMatch = content.match(/###\s*Task\s*\d+/g);
+        const taskCount = taskMatch ? taskMatch.length : 0;
+        const decisionMatch = content.match(/decision/gi);
+        const hasDecisions = decisionMatch !== null && decisionMatch.length > 0;
+        // Count file mentions
+        const fileMentions = new Set();
+        const filePattern = /`([^`]+\.[a-zA-Z]+)`/g;
+        let m;
+        while ((m = filePattern.exec(content)) !== null) {
+            if (m[1].includes('/') && !m[1].startsWith('http')) {
+                fileMentions.add(m[1]);
+            }
+        }
+        const fileCount = fileMentions.size;
+        let template = 'templates/summary-standard.md';
+        let type = 'standard';
+        if (taskCount <= 2 && fileCount <= 3 && !hasDecisions) {
+            template = 'templates/summary-minimal.md';
+            type = 'minimal';
+        }
+        else if (hasDecisions || fileCount > 6 || taskCount > 5) {
+            template = 'templates/summary-complex.md';
+            type = 'complex';
+        }
+        const result = { template, type, taskCount, fileCount, hasDecisions };
+        output(result, raw, template);
+    }
+    catch (e) {
+        // Fallback to standard -- include error_type for diagnostics
+        const err = e;
+        const errorType = err.code === 'ENOENT' ? 'file_not_found' : 'read_error';
+        const result = {
+            template: 'templates/summary-standard.md',
+            type: 'standard',
+            taskCount: 0,
+            fileCount: 0,
+            hasDecisions: false,
+            error: err.message,
+            error_type: errorType,
+        };
+        output(result, raw, 'templates/summary-standard.md');
+    }
+}
+// ─── Template Fill ──────────────────────────────────────────────────────────
+/**
+ * CLI command: Fill a template (summary, plan, or verification) with values and write to disk.
+ * @param cwd - Project working directory
+ * @param templateType - Template type: 'summary', 'plan', or 'verification'
+ * @param options - Template options
+ * @param raw - Output raw file path instead of JSON
+ */
+function cmdTemplateFill(cwd, templateType, options, raw) {
+    if (!templateType) {
+        error('template type required: summary, plan, or verification. Usage: scaffold <summary|plan|verification> --phase <N> --plan <M>. Specify a template type, e.g.: scaffold summary. Valid types: summary, plan, verification, context, uat, baseline. To list available templates: scaffold template-select <type>');
+    }
+    if (!options.phase) {
+        error('--phase required');
+        return; // unreachable but helps TS narrowing
+    }
+    const phaseNum = options.phase;
+    const phaseInfo = findPhaseInternal(cwd, phaseNum);
+    if (!phaseInfo || !phaseInfo.found) {
+        output({ error: 'Phase not found', phase: phaseNum }, raw);
+        return;
+    }
+    const padded = normalizePhaseName(phaseNum);
+    const today = new Date().toISOString().split('T')[0];
+    const phaseName = options.name || phaseInfo.phase_name || 'Unnamed';
+    const phaseSlug = phaseInfo.phase_slug || generateSlugInternal(phaseName) || 'unnamed';
+    const phaseId = `${padded}-${phaseSlug}`;
+    const planNum = (options.plan || '01').padStart(2, '0');
+    const fields = options.fields || {};
+    let frontmatter;
+    let body;
+    let fileName;
+    switch (templateType) {
+        case 'summary': {
+            frontmatter = {
+                phase: phaseId,
+                plan: planNum,
+                subsystem: '[primary category]',
+                tags: [],
+                provides: [],
+                affects: [],
+                'tech-stack': { added: [], patterns: [] },
+                'key-files': { created: [], modified: [] },
+                'key-decisions': [],
+                'patterns-established': [],
+                duration: '[X]min',
+                completed: today,
+                ...fields,
+            };
+            body = [
+                `# Phase ${options.phase}: ${phaseName} Summary`,
+                '',
+                '**[Substantive one-liner describing outcome]**',
+                '',
+                '## Performance',
+                '- **Duration:** [time]',
+                '- **Tasks:** [count completed]',
+                '- **Files modified:** [count]',
+                '',
+                '## Accomplishments',
+                '- [Key outcome 1]',
+                '- [Key outcome 2]',
+                '',
+                '## Task Commits',
+                '1. **Task 1: [task name]** - `hash`',
+                '',
+                '## Files Created/Modified',
+                '- `path/to/file.ts` - What it does',
+                '',
+                '## Decisions & Deviations',
+                '[Key decisions or "None - followed plan as specified"]',
+                '',
+                '## Next Phase Readiness',
+                "[What's ready for next phase]",
+            ].join('\n');
+            fileName = `${padded}-${planNum}-SUMMARY.md`;
+            break;
+        }
+        case 'plan': {
+            const planType = options.type || 'execute';
+            const wave = parseInt(options.wave || '1') || 1;
+            frontmatter = {
+                phase: phaseId,
+                plan: planNum,
+                type: planType,
+                wave,
+                depends_on: [],
+                files_modified: [],
+                autonomous: true,
+                user_setup: [],
+                must_haves: { truths: [], artifacts: [], key_links: [] },
+                ...fields,
+            };
+            body = [
+                `# Phase ${options.phase} Plan ${planNum}: [Title]`,
+                '',
+                '## Objective',
+                '- **What:** [What this plan builds]',
+                '- **Why:** [Why it matters for the phase goal]',
+                '- **Output:** [Concrete deliverable]',
+                '',
+                '## Context',
+                '@.planning/PROJECT.md',
+                '@.planning/ROADMAP.md',
+                '@.planning/STATE.md',
+                '',
+                '## Tasks',
+                '',
+                '<task type="code">',
+                '  <name>[Task name]</name>',
+                '  <files>[file paths]</files>',
+                '  <action>[What to do]</action>',
+                '  <verify>[How to verify]</verify>',
+                '  <done>[Definition of done]</done>',
+                '</task>',
+                '',
+                '## Verification',
+                '[How to verify this plan achieved its objective]',
+                '',
+                '## Success Criteria',
+                '- [ ] [Criterion 1]',
+                '- [ ] [Criterion 2]',
+            ].join('\n');
+            fileName = `${padded}-${planNum}-PLAN.md`;
+            break;
+        }
+        case 'verification': {
+            frontmatter = {
+                phase: phaseId,
+                verified: new Date().toISOString(),
+                status: 'pending',
+                score: '0/0 must-haves verified',
+                ...fields,
+            };
+            body = [
+                `# Phase ${options.phase}: ${phaseName} -- Verification`,
+                '',
+                '## Observable Truths',
+                '| # | Truth | Status | Evidence |',
+                '|---|-------|--------|----------|',
+                '| 1 | [Truth] | pending | |',
+                '',
+                '## Required Artifacts',
+                '| Artifact | Expected | Status | Details |',
+                '|----------|----------|--------|---------|',
+                '| [path] | [what] | pending | |',
+                '',
+                '## Key Link Verification',
+                '| From | To | Via | Status | Details |',
+                '|------|----|----|--------|---------|',
+                '| [source] | [target] | [connection] | pending | |',
+                '',
+                '## Requirements Coverage',
+                '| Requirement | Status | Blocking Issue |',
+                '|-------------|--------|----------------|',
+                '| [req] | pending | |',
+                '',
+                '## Result',
+                '[Pending verification]',
+            ].join('\n');
+            fileName = `${padded}-VERIFICATION.md`;
+            break;
+        }
+        default:
+            error(`Unknown template type: ${templateType}. Available: summary, plan, verification. Usage: scaffold <summary|plan|verification> --phase <N> --plan <M>. Use one of: summary, plan, or verification.`);
+            return;
+    }
+    const fullContent = `---\n${reconstructFrontmatter(frontmatter)}\n---\n\n${body}\n`;
+    const outPath = path.join(cwd, phaseInfo.directory, fileName);
+    if (fs.existsSync(outPath)) {
+        output({ error: 'File already exists', path: path.relative(cwd, outPath) }, raw);
+        return;
+    }
+    fs.writeFileSync(outPath, fullContent, 'utf-8');
+    const relPath = path.relative(cwd, outPath);
+    const result = { created: true, path: relPath, template: templateType };
+    output(result, raw, relPath);
+}
+// ─── Scaffold ───────────────────────────────────────────────────────────────
+/**
+ * CLI command: Scaffold directory structures and files for various GRD artifact types.
+ * @param cwd - Project working directory
+ * @param type - Scaffold type: 'context', 'uat', 'verification', 'phase-dir', 'research-dir', 'eval', or 'baseline'
+ * @param options - Scaffold options
+ * @param raw - Output raw file path instead of JSON
+ */
+function cmdScaffold(cwd, type, options, raw) {
+    const { phase, name } = options;
+    const padded = phase ? normalizePhaseName(phase) : '00';
+    const today = new Date().toISOString().split('T')[0];
+    // Find phase directory
+    const phaseInfo = phase ? findPhaseInternal(cwd, phase) : null;
+    const phaseDir = phaseInfo ? path.join(cwd, phaseInfo.directory) : null;
+    if (phase && !phaseDir && type !== 'phase-dir') {
+        error(`Phase ${phase} directory not found. Run "scaffold phase-dir --phase ${phase} --name <description>" to create it, or check .planning/milestones/ for existing phases`);
+    }
+    let filePath;
+    let content;
+    switch (type) {
+        case 'context': {
+            filePath = path.join(phaseDir, `${padded}-CONTEXT.md`);
+            content = `---\nphase: "${padded}"\nname: "${name || phaseInfo?.phase_name || 'Unnamed'}"\ncreated: ${today}\n---\n\n# Phase ${phase}: ${name || phaseInfo?.phase_name || 'Unnamed'} -- Context\n\n## Decisions\n\n_Decisions will be captured during /grd:discuss-phase ${phase}_\n\n## Discretion Areas\n\n_Areas where the executor can use judgment_\n\n## Deferred Ideas\n\n_Ideas to consider later_\n`;
+            break;
+        }
+        case 'uat': {
+            filePath = path.join(phaseDir, `${padded}-UAT.md`);
+            content = `---\nphase: "${padded}"\nname: "${name || phaseInfo?.phase_name || 'Unnamed'}"\ncreated: ${today}\nstatus: pending\n---\n\n# Phase ${phase}: ${name || phaseInfo?.phase_name || 'Unnamed'} -- User Acceptance Testing\n\n## Test Results\n\n| # | Test | Status | Notes |\n|---|------|--------|-------|\n\n## Summary\n\n_Pending UAT_\n`;
+            break;
+        }
+        case 'verification': {
+            filePath = path.join(phaseDir, `${padded}-VERIFICATION.md`);
+            content = `---\nphase: "${padded}"\nname: "${name || phaseInfo?.phase_name || 'Unnamed'}"\ncreated: ${today}\nstatus: pending\n---\n\n# Phase ${phase}: ${name || phaseInfo?.phase_name || 'Unnamed'} -- Verification\n\n## Goal-Backward Verification\n\n**Phase Goal:** [From ROADMAP.md]\n\n## Checks\n\n| # | Requirement | Status | Evidence |\n|---|------------|--------|----------|\n\n## Result\n\n_Pending verification_\n`;
+            break;
+        }
+        case 'phase-dir': {
+            if (!phase || !name) {
+                error('phase and name required for phase-dir scaffold. Usage: scaffold phase-dir --phase <N> --name <description>. Provide both flags, e.g.: scaffold phase-dir --phase 3 --name "Data Preprocessing"');
+            }
+            const slug = generateSlugInternal(name);
+            const dirName = `${padded}-${slug}`;
+            const phasesParent = getPhasesDirPath(cwd);
+            fs.mkdirSync(phasesParent, { recursive: true });
+            const dirPath = path.join(phasesParent, dirName);
+            fs.mkdirSync(dirPath, { recursive: true });
+            const result = {
+                created: true,
+                directory: path.relative(cwd, dirPath),
+                path: dirPath,
+            };
+            output(result, raw, dirPath);
+            return;
+        }
+        case 'research-dir': {
+            const researchDir = getResearchDirPath(cwd);
+            const deepDivesDir = path.join(researchDir, 'deep-dives');
+            fs.mkdirSync(deepDivesDir, { recursive: true });
+            const result = {
+                created: true,
+                directory: path.relative(cwd, researchDir) + '/',
+            };
+            output(result, raw, researchDir);
+            return;
+        }
+        case 'eval': {
+            filePath = path.join(phaseDir, `${padded}-EVAL.md`);
+            content = `---\nphase: "${padded}"\nname: "${name || phaseInfo?.phase_name || 'Unnamed'}"\ncreated: ${today}\nstatus: pending\nverification_level: proxy\n---\n\n# Phase ${phase}: ${name || phaseInfo?.phase_name || 'Unnamed'} -- Evaluation Plan\n\n## Metrics\n\n| Metric | Baseline | Target | Level |\n|--------|----------|--------|-------|\n\n## Datasets\n\n## Protocol\n\n## Deferred Validations\n\n_Validations that cannot be run until integration phase_\n`;
+            break;
+        }
+        case 'baseline': {
+            const baselinePath = path.join(cwd, '.planning', 'BASELINE.md');
+            if (fs.existsSync(baselinePath)) {
+                const result = {
+                    created: false,
+                    reason: 'already_exists',
+                    path: baselinePath,
+                };
+                output(result, raw, 'exists');
+                return;
+            }
+            const baselineContent = `# Baseline Assessment\n\n**Assessed:** ${today}\n\n## Current Metrics\n\n| Metric | Value | Method | Notes |\n|--------|-------|--------|-------|\n\n## Environment\n\n## Quality Summary\n`;
+            fs.writeFileSync(baselinePath, baselineContent, 'utf-8');
+            const result = {
+                created: true,
+                path: path.relative(cwd, path.join(getPlanningDir(cwd), 'BASELINE.md')),
+            };
+            output(result, raw, baselinePath);
+            return;
+        }
+        default:
+            error(`Unknown scaffold type: ${type}. Available: context, uat, verification, phase-dir, research-dir, eval, baseline. Usage: scaffold <type> --phase <N>. Use one of: context, uat, verification, phase-dir, research-dir, eval, or baseline.`);
+    }
+    if (filePath && fs.existsSync(filePath)) {
+        const result = { created: false, reason: 'already_exists', path: filePath };
+        output(result, raw, 'exists');
+        return;
+    }
+    if (filePath && content) {
+        fs.writeFileSync(filePath, content, 'utf-8');
+        const relPath = path.relative(cwd, filePath);
+        const result = { created: true, path: relPath };
+        output(result, raw, relPath);
+    }
+}
+// ─── Exports ────────────────────────────────────────────────────────────────
+module.exports = {
+    cmdTemplateSelect,
+    cmdTemplateFill,
+    cmdScaffold,
+};
+//# sourceMappingURL=scaffold.js.map

package/dist/lib/scaffold.js.map

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

@@ -0,0 +1,11 @@
+/**
+ * Read a file as UTF-8, returning null on I/O error. Writes a warning to
+ * stderr describing the failure.
+ */
+export declare function _readUtf8OrNull(file: string): string | null;
+/**
+ * Truncate a string to at most `max` characters, appending "..." if trimmed.
+ * Used to cap the `match` field on ScanHit for display output.
+ */
+export declare function _truncate(s: string, max: number): string;
+//# sourceMappingURL=_utils.d.ts.map

package/dist/lib/scan/_utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"_utils.d.ts","sourceRoot":"","sources":["../../../lib/scan/_utils.ts"],"names":[],"mappings":"AAYA;;;GAGG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAS3D;AAED;;;GAGG;AACH,wBAAgB,SAAS,CAAC,CAAC,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,CAGxD"}

package/dist/lib/scan/_utils.js

@@ -0,0 +1,36 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports._readUtf8OrNull = _readUtf8OrNull;
+exports._truncate = _truncate;
+/**
+ * GRD Scan/Utils -- Shared internal helpers for the prompt injection scanners.
+ *
+ * These helpers are used by both scanProse (injection.ts) and scanBase64
+ * (base64.ts). The underscore-prefix filename signals "internal to the scan
+ * module, not a public API" per GRD convention.
+ */
+const fs = require("fs");
+/**
+ * Read a file as UTF-8, returning null on I/O error. Writes a warning to
+ * stderr describing the failure.
+ */
+function _readUtf8OrNull(file) {
+    try {
+        return fs.readFileSync(file, "utf8");
+    }
+    catch (e) {
+        process.stderr.write(`warning: cannot read ${file}: ${e.message}\n`);
+        return null;
+    }
+}
+/**
+ * Truncate a string to at most `max` characters, appending "..." if trimmed.
+ * Used to cap the `match` field on ScanHit for display output.
+ */
+function _truncate(s, max) {
+    if (s.length <= max)
+        return s;
+    return s.slice(0, max) + "...";
+}
+module.exports = { _readUtf8OrNull, _truncate };
+//# sourceMappingURL=_utils.js.map

package/dist/lib/scan/_utils.js.map

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package/dist/lib/scan/base64.d.ts

@@ -0,0 +1,15 @@
+/**
+ * GRD Scan/Base64 -- Detect prompt injection patterns hidden inside
+ * base64-encoded blobs.
+ *
+ * Extracts contiguous base64-alphabet runs of >=40 chars from each file,
+ * attempts UTF-8 decoding, and applies the same INJECTION_PATTERNS to the
+ * decoded text. Matches gsd-2 v2.67 scripts/base64-scan.sh threshold.
+ */
+import type { IgnoreEntry } from "./ignorefile";
+import type { ScanHit } from "./types";
+export interface ScanBase64Opts {
+    ignoreEntries: IgnoreEntry[];
+}
+export declare function scanBase64(files: string[], opts: ScanBase64Opts): ScanHit[];
+//# sourceMappingURL=base64.d.ts.map

package/dist/lib/scan/base64.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/scan/base64.js

@@ -0,0 +1,66 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.scanBase64 = scanBase64;
+const { INJECTION_PATTERNS } = require("./patterns");
+const { isIgnored } = require("./ignorefile");
+const { _readUtf8OrNull, _truncate } = require("./_utils");
+const BASE64_RUN_RE = /[A-Za-z0-9+/=]{40,}/g;
+const MIN_BASE64_LEN = 40;
+function scanBase64(files, opts) {
+    const hits = [];
+    for (const file of files) {
+        const raw = _readUtf8OrNull(file);
+        if (raw === null)
+            continue;
+        const lines = raw.split("\n");
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i];
+            const candidates = line.match(BASE64_RUN_RE);
+            if (!candidates)
+                continue;
+            for (const candidate of candidates) {
+                if (candidate.length < MIN_BASE64_LEN)
+                    continue;
+                const decoded = _tryDecodeUtf8(candidate);
+                if (decoded === null)
+                    continue;
+                for (const pattern of INJECTION_PATTERNS) {
+                    const m = decoded.match(pattern.regex);
+                    if (m) {
+                        const match = _truncate(m[0], 80);
+                        hits.push({
+                            file,
+                            line: i + 1,
+                            pattern: pattern.id,
+                            label: pattern.label,
+                            category: pattern.category,
+                            match,
+                            ignored: isIgnored(file, decoded, opts.ignoreEntries),
+                            source: "base64",
+                        });
+                    }
+                }
+            }
+        }
+    }
+    return hits;
+}
+// ─── Helpers ──────────────────────────────────────────────────────────────────
+function _tryDecodeUtf8(candidate) {
+    try {
+        const buf = Buffer.from(candidate, "base64");
+        const normalized = candidate.replace(/=+$/, "");
+        const reencoded = buf.toString("base64").replace(/=+$/, "");
+        if (reencoded !== normalized)
+            return null;
+        const decoded = buf.toString("utf8");
+        if (decoded.includes("\uFFFD"))
+            return null;
+        return decoded;
+    }
+    catch {
+        return null;
+    }
+}
+module.exports = { scanBase64 };
+//# sourceMappingURL=base64.js.map

package/dist/lib/scan/base64.js.map

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package/dist/lib/scan/ignorefile.d.ts

@@ -0,0 +1,30 @@
+export type IgnoreEntry = {
+    type: "file";
+    filePath: string;
+    pattern: RegExp;
+} | {
+    type: "global";
+    pattern: RegExp;
+};
+export declare function parseIgnoreFile(raw: string): IgnoreEntry[];
+export declare function loadIgnoreFile(filePath: string): IgnoreEntry[];
+/**
+ * Check whether a hit should be suppressed by any ignorefile entry.
+ *
+ * The `matchText` parameter is the SCANNED content that produced the hit:
+ *   - For prose hits: the full source line
+ *   - For base64 hits: the full decoded content of the base64 blob
+ *
+ * This is intentionally wider than the reported `match` field on ScanHit
+ * (which is truncated to 80 chars for display). Ignorefile entries should
+ * be written against the scanned content — see `.prompt-injection-scanignore`
+ * for examples.
+ *
+ * @param file - the file where the hit was found (may be absolute or relative;
+ *   suffix-matching supported)
+ * @param matchText - the scanned content (full source line or full decoded blob)
+ * @param entries - parsed ignorefile entries from loadIgnoreFile
+ * @returns true if any entry matches and the hit should be suppressed
+ */
+export declare function isIgnored(file: string, matchText: string, entries: IgnoreEntry[]): boolean;
+//# sourceMappingURL=ignorefile.d.ts.map

package/dist/lib/scan/ignorefile.d.ts.map

@@ -0,0 +1 @@
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