@dotdotgod/cli 0.2.3 → 0.2.5

package/README.md

@@ -33,12 +33,12 @@ dotdotgod graph impact . --changed <path> --compact
 
 ## What It Does
 
-- `init` creates `AGENTS.md`, thin agent entrypoints, docs indexes, active-plan space, archive map, and local cache ignores.
+- `init` creates `AGENTS.md`, thin agent entrypoints, docs indexes, active-plan space, archive map, local cache ignores, and the complete editable default config.
 - `validate` checks the dotdotgod docs/project-memory structure, local links, traceability blocks, config validity, and optional index freshness.
 - `index` builds `.dotdotgod/manifest.json` and compact graph shards from maintained project files.
 - `load-snapshot` returns a bounded first-pass project map for AI agents, including files pinned through the `load.pinnedPaths`/`load.pinnedBodies` config so context such as code conventions stays visible on every load.
 - `resolve` and `expand` map explicit or high-signal prompt references to project files.
-- `graph impact` ranks likely related specs, tests, docs, commands, and source files for a changed path.
+- `graph impact` ranks likely related specs, tests, docs, commands, and source files for one or more changed paths, with a combined ranking and per-file top five.
 - `traceability links` checks or repairs generated Markdown traceability-link sections.
 - `plan validate` validates active plan artifacts and simplified Plan Generator checkpoints before execution.
 - `plan stage create` creates an internal `.dotdotgod-plan/NN_STAGE_NAME.md` checkpoint for a simplified Plan Generator stage.
@@ -66,8 +66,8 @@ dotdotgod plan validate docs/plan/<task-slug>/README.md
 dotdotgod plan validate docs/plan/<task-slug>/README.md --stage 04
 dotdotgod plan stage create 02 docs/plan/<task-slug>/README.md
 dotdotgod graph impact . --changed <path>
-dotdotgod graph impact . --changed <path> --compact
-dotdotgod graph impact . --changed <path> --yml
+dotdotgod graph impact . --changed <path> --changed <another-path> --compact
+dotdotgod graph impact . --changed <path> --changed <another-path> --yml
 dotdotgod graph communities .
 ```
 
@@ -104,7 +104,7 @@ files:
 - packages/pi/extensions/plan-mode/index.ts (45; implemented_by, semantic_similarity)
 ```
 
-`graph impact` needs `--changed <path>` so ranking has a seed file. Use `--compact` for short text, `--yml` or `--yaml` for compact structured agent-facing output, and `--json` for machine-readable detail.
+`graph impact` needs at least one `--changed <path>` and accepts repeated options. Multi-file output preserves input order, deduplicates repeated paths, returns a bounded combined ranking, and includes the top five non-seed results for each changed file. Use `--compact` for short text, `--yml` or `--yaml` for compact structured agent-facing output, and `--json` for machine-readable detail.
 
 The graph is built from maintained project files: Markdown links, README routes, headings, traceability blocks, package metadata, memory areas, imports, exports, commands, tests, and deterministic routing hints.
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@dotdotgod/cli",
-  "version": "0.2.3",
+  "version": "0.2.5",
   "description": "CLI for dotdotgod validation, project memory snapshots, and graph indexing.",
   "type": "module",
   "license": "Elastic-2.0",

package/src/cli/usage.mjs

@@ -81,13 +81,13 @@ Write mode:
 Checks or writes generated Markdown traceability link sections from canonical fenced json dotdotgod blocks.`;
     case 'graph':
       return `Usage:
-  dotdotgod graph impact <root> --changed <path> [--compact|--json|--yml|--yaml]
+  dotdotgod graph impact <root> --changed <path> [--changed <path> ...] [--compact|--json|--yml|--yaml]
   dotdotgod graph communities <root> [--json]`;
     case 'graph impact':
       return `Usage:
-  dotdotgod graph impact <root> --changed <path> [--compact|--json|--yml|--yaml]
+  dotdotgod graph impact <root> --changed <path> [--changed <path> ...] [--compact|--json|--yml|--yaml]
 
-Ranks nodes related to a changed file. <root> is the project root; --changed is a project-relative file path. Use --compact for a short text summary or --yml/--yaml for structured agent-facing output.`;
+Ranks nodes related to one or more changed files. <root> is the project root; repeat --changed with project-relative file paths. Results include a combined ranking and the top five related nodes for each changed file. Use --compact for a short text summary or --yml/--yaml for structured agent-facing output.`;
     case 'graph communities':
       return `Usage:
   dotdotgod graph communities <root> [--json]`;
@@ -109,7 +109,7 @@ Ranks nodes related to a changed file. <root> is the project root; --changed is
   dotdotgod plan validate docs/plan/<task-slug>/README.md [--stage stage] [--json]
   dotdotgod plan stage create <stage> [docs/plan/<task-slug>/README.md] [--json]
   dotdotgod trello sync <root> [--dry-run]
-  dotdotgod graph impact <root> --changed <path> [--compact|--json|--yml|--yaml]
+  dotdotgod graph impact <root> --changed <path> [--changed <path> ...] [--compact|--json|--yml|--yaml]
   dotdotgod graph communities <root> [--json]`;
   }
 }

package/src/commands/graph.mjs

@@ -4,16 +4,18 @@ import { graphSummary, readFreshIndex } from '../index/cache.mjs';
 import { buildCompactImpactReport, buildImpactReport } from '../impact/report.mjs';
 import { formatCompactImpactOutput, formatYmlGraphImpactError, formatYmlImpactOutput } from '../impact/format.mjs';
 
+const MAX_CHANGED_FILES = 20;
+
 export function parseGraphOptions(argv) {
   const filtered = [];
-  let changed;
+  const changed = [];
   let compact = false;
   let yml = false;
   for (let i = 0; i < argv.length; i += 1) {
     if (argv[i] === '--changed') {
       const next = argv[i + 1];
       if (next && !next.startsWith('-')) {
-        changed = next;
+        changed.push(next);
         i += 1;
       }
     } else if (argv[i] === '--compact') compact = true;
@@ -21,13 +23,13 @@ export function parseGraphOptions(argv) {
     else filtered.push(argv[i]);
   }
   const options = parseCommon(filtered);
-  options.changed = changed;
+  options.changed = [...new Set(changed)];
   options.compact = compact;
   options.yml = yml;
   return options;
 }
 
-export function runGraph(argv) {
+export async function runGraph(argv) {
   const sub = argv[0];
   const isImpact = sub === 'impact';
   if (!['impact', 'communities'].includes(sub)) usage(sub ? `Unknown graph command: ${sub}` : 'Missing graph command.', 'graph');
@@ -39,7 +41,7 @@ export function runGraph(argv) {
     else usage(message, 'graph impact');
     process.exit(2);
   }
-  if (isImpact && !options.changed) {
+  if (isImpact && options.changed.length === 0) {
     const message = 'Missing required option: --changed <path>. Run `dotdotgod graph impact <root> --changed <path>`.';
     if (options.json) {
       console.log(JSON.stringify({ ok: false, command: 'graph impact', compact: options.compact || undefined, root: options.root, error: { code: 'MISSING_CHANGED', message }, usage: commandUsage('graph impact') }, null, 2));
@@ -51,11 +53,23 @@ export function runGraph(argv) {
     }
     usage(message, 'graph impact');
   }
+  if (isImpact && options.changed.length > MAX_CHANGED_FILES) {
+    const message = `Too many changed files: received ${options.changed.length}; maximum is ${MAX_CHANGED_FILES}.`;
+    if (options.json) {
+      console.log(JSON.stringify({ ok: false, command: 'graph impact', root: options.root, error: { code: 'TOO_MANY_CHANGED', message }, usage: commandUsage('graph impact') }, null, 2));
+      process.exit(2);
+    }
+    if (options.yml) {
+      console.log(formatYmlGraphImpactError(options, message, 'TOO_MANY_CHANGED'));
+      process.exit(2);
+    }
+    usage(message, 'graph impact');
+  }
   const { status, index, metadata } = readFreshIndex(options.root);
   const rawImpact = isImpact ? buildImpactReport(index, options.changed) : undefined;
   const impact = isImpact && (options.compact || options.yml) ? buildCompactImpactReport(rawImpact) : rawImpact;
   const payload = isImpact
-    ? { ok: status.ok, command: 'graph impact', compact: options.compact || undefined, root: options.root, status, metadata, changed: options.changed, related: impact.related, impact }
+    ? { ok: status.ok, command: 'graph impact', compact: options.compact || undefined, root: options.root, status, metadata, changed: options.changed[0], changedFiles: options.changed, related: impact.related, impact }
     : { ok: status.ok, command: 'graph communities', root: options.root, status, metadata, graph: graphSummary(index), communities: buildCommunities(index) };
   const refreshNote = metadata.cacheRefreshed ? ', refreshed' : '';
   if (options.json) console.log(JSON.stringify(payload, null, 2));

package/src/core.mjs

@@ -57,7 +57,7 @@ export async function runCli(argv = process.argv.slice(2)) {
   else if (command === 'resolve') runResolve(args);
   else if (command === 'expand') runExpand(args);
   else if (command === 'traceability') runTraceability(args);
-  else if (command === 'graph') runGraph(args);
+  else if (command === 'graph') await runGraph(args);
   else if (command === 'plan') runPlan(args);
   else if (command === 'trello') {
     const result = await Promise.resolve(runTrelloSync(args));

package/src/impact/format.mjs

@@ -15,7 +15,8 @@ function formatCompactImpactGroup(name, group) {
 
 export function formatCompactImpactOutput(payload, impact) {
   const refreshNote = payload.metadata.cacheRefreshed ? ', refreshed' : '';
-  const lines = [`graph impact compact: ${impact.related.length} related node(s), ${impact.omittedRelated ?? 0} omitted (${payload.status.status}${refreshNote} index)`];
+  const lines = [`graph impact compact: ${impact.related.length} related node(s), ${impact.omittedRelated ?? 0} omitted (${payload.status.status}${refreshNote} index)`, `changed files: ${(impact.changedFiles ?? [impact.changed]).join(', ')}`];
+  for (const entry of impact.perSeed ?? []) lines.push(...formatCompactImpactGroup(`top for ${entry.changed}`, { items: entry.related }));
   for (const name of ['docs', 'contracts', 'tests', 'files', 'commands', 'events', 'packageResources', 'symbols']) lines.push(...formatCompactImpactGroup(name, impact.groups[name]));
   return lines.join('\n');
 }
@@ -58,6 +59,7 @@ export function formatYmlImpactOutput(payload, impact) {
     'impact:',
     `  ok: ${payload.ok ? 'true' : 'false'}`,
     `  changed: ${ymlScalar(payload.changed)}`,
+    `  changed_files: ${ymlList(payload.changedFiles ?? [payload.changed])}`,
     `  root: ${ymlScalar(payload.root)}`,
     '  output: "yml"',
     '  status:',
@@ -69,8 +71,16 @@ export function formatYmlImpactOutput(payload, impact) {
     `    method: ${ymlScalar(impact.ranking?.method)}`,
     `    preset: ${ymlScalar(impact.ranking?.preset)}`,
     `    config_source: ${ymlScalar(impact.ranking?.configSource)}`,
-    '  groups:',
+    '  per_seed:',
   ];
+  for (const entry of impact.perSeed ?? []) {
+    lines.push(`    - changed: ${ymlScalar(entry.changed)}`);
+    lines.push(`      omitted_related: ${entry.omittedRelated ?? 0}`);
+    lines.push('      related:');
+    if ((entry.related ?? []).length === 0) lines.push('        []');
+    else for (const item of entry.related) lines.push(...formatYmlImpactItem(item));
+  }
+  lines.push('  groups:');
   for (const name of ['docs', 'contracts', 'tests', 'files', 'commands', 'events', 'packageResources', 'symbols']) lines.push(...formatYmlImpactGroup(name, impact.groups[name]));
   lines.push('  recommended_actions:');
   lines.push('    - "review_related_docs"');

package/src/impact/report.mjs

@@ -11,7 +11,13 @@ function addImpactItem(group, item, limit = 10) {
   group.items.push(item);
 }
 
-function selectImpactItems(sortedItems, maxRelated, seed) {
+function normalizeChangedPaths(changedPaths) {
+  const values = Array.isArray(changedPaths) ? changedPaths : [changedPaths];
+  return [...new Set(values.filter((value) => typeof value === 'string' && value.length > 0))];
+}
+
+function selectImpactItems(sortedItems, maxRelated, seeds) {
+  const seedSet = new Set(seeds);
   const selected = [];
   const selectedIds = new Set();
   const deferred = [];
@@ -22,35 +28,36 @@ function selectImpactItems(sortedItems, maxRelated, seed) {
   const add = (item, force = false) => {
     if (selected.length >= maxRelated || selectedIds.has(item.id)) return;
     const pathKey = item.path ?? item.id;
-    if (!force && item.id !== seed && selected.length < firstPageLimit) {
+    if (!force && !seedSet.has(item.id) && selected.length < firstPageLimit) {
       if (pathKey && (firstPagePathCounts.get(pathKey) ?? 0) >= 2) return deferred.push(item);
       if (isLowActionabilityImpactItem(item) && lowActionabilityInFirstPage >= 2) return deferred.push(item);
       if (isSemanticOnlyImpactItem(item) && semanticOnlyInFirstPage >= 3) return deferred.push(item);
     }
     selected.push(item);
     selectedIds.add(item.id);
-    if (selected.length <= firstPageLimit && item.id !== seed) {
+    if (selected.length <= firstPageLimit && !seedSet.has(item.id)) {
       if (pathKey) firstPagePathCounts.set(pathKey, (firstPagePathCounts.get(pathKey) ?? 0) + 1);
       if (isLowActionabilityImpactItem(item)) lowActionabilityInFirstPage += 1;
       if (isSemanticOnlyImpactItem(item)) semanticOnlyInFirstPage += 1;
     }
   };
-  for (const item of sortedItems) if (item.id === seed) add(item, true);
-  for (const item of sortedItems) if (item.id !== seed) add(item);
+  for (const item of sortedItems) if (seedSet.has(item.id)) add(item, true);
+  for (const item of sortedItems) if (!seedSet.has(item.id)) add(item);
   for (const item of deferred) add(item, true);
   return selected;
 }
 
-export function buildImpactReport(index, changedPath, limits = {}) {
+function buildCombinedImpactReport(index, changedPaths, limits = {}) {
   const graph = index?.graph ?? { nodes: [], edges: [] };
   const config = index?.memoryConfig ? { ...defaultMemoryConfig(), ...index.memoryConfig } : defaultMemoryConfig();
   const policy = cloneImpactRankingPolicy(config.impactRanking ?? DEFAULT_IMPACT_RANKING_POLICY);
   const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));
-  const seed = `file:${changedPath}`;
-  const maxRelated = limits.related ?? 25;
+  const seeds = changedPaths.map((path) => `file:${path}`);
+  const seedSet = new Set(seeds);
+  const maxRelated = Math.max(limits.related ?? 25, seeds.length);
   const groups = { files: { items: [], omitted: 0 }, docs: { items: [], omitted: 0 }, contracts: { items: [], omitted: 0 }, tests: { items: [], omitted: 0 }, commands: { items: [], omitted: 0 }, events: { items: [], omitted: 0 }, packageResources: { items: [], omitted: 0 }, symbols: { items: [], omitted: 0 } };
-  const relatedIds = new Set([seed]);
-  const reasons = new Map([[seed, new Set(['changed-file'])]]);
+  const relatedIds = new Set(seeds);
+  const reasons = new Map(seeds.map((seed) => [seed, new Set(['changed-file'])]));
   const addReason = (id, reason) => {
     relatedIds.add(id);
     if (!reasons.has(id)) reasons.set(id, new Set());
@@ -58,27 +65,27 @@ export function buildImpactReport(index, changedPath, limits = {}) {
   };
 
   for (const edge of graph.edges) {
-    if (edge.source === seed) addReason(edge.target, edge.relation);
-    if (edge.target === seed) addReason(edge.source, `incoming:${edge.relation}`);
+    if (seedSet.has(edge.source)) addReason(edge.target, edge.relation);
+    if (seedSet.has(edge.target)) addReason(edge.source, `incoming:${edge.relation}`);
   }
   const expansionRelations = new Set(['implemented_by', 'verified_by', 'related_doc', 'verification_command', ...SEMANTIC_RELATIONS]);
   for (const edge of graph.edges) {
     if (!expansionRelations.has(edge.relation)) continue;
-    if (relatedIds.has(edge.source) && edge.target !== seed) addReason(edge.target, edge.relation);
+    if (relatedIds.has(edge.source) && !seedSet.has(edge.target)) addReason(edge.target, edge.relation);
   }
 
-  const pprScores = buildPersonalizedPageRank(graph, seed, policy);
-  const candidatePprMax = Math.max(0, ...[...relatedIds].filter((id) => id !== seed).map((id) => pprScores.get(id) ?? 0));
+  const pprScores = buildPersonalizedPageRank(graph, seeds, policy);
+  const candidatePprMax = Math.max(0, ...[...relatedIds].filter((id) => !seedSet.has(id)).map((id) => pprScores.get(id) ?? 0));
   const relatedAll = [...relatedIds].map((id) => {
     const node = nodeById.get(id) ?? { id };
     const path = node.path ?? id.replace(/^file:/, '').replace(/^test:/, '');
     const reasonList = [...(reasons.get(id) ?? [])];
     const retrieval = node.retrieval ?? retrievalMetadataForPath(path);
     const reasonSignals = reasonList.map((reason) => `reason:${reason}`);
-    const scored = scoreImpactItem({ ...node, reasons: reasonList, retrieval }, seed, changedPath, policy, pprScores, candidatePprMax);
+    const scored = scoreImpactItem({ ...node, reasons: reasonList, retrieval }, seedSet, changedPaths, policy, pprScores, candidatePprMax);
     return { ...node, reasons: reasonList, retrieval: { ...retrieval, signals: [...new Set([...(retrieval.signals ?? []), ...reasonSignals])] }, ...scored };
-  }).sort(compareImpactItems(seed));
-  const related = selectImpactItems(relatedAll, maxRelated, seed);
+  }).sort(compareImpactItems(seeds));
+  const related = selectImpactItems(relatedAll, maxRelated, seeds);
   for (const item of related) {
     if (item.type === 'file') {
       const area = docsArea(item.path);
@@ -91,7 +98,19 @@ export function buildImpactReport(index, changedPath, limits = {}) {
     else if (item.type === 'event') addImpactItem(groups.events, item, limits.events ?? 10);
     else if (item.type === 'package_resource') addImpactItem(groups.packageResources, item, limits.packageResources ?? 10);
   }
-  return { changed: changedPath, ranking: { method: policy.ppr.enabled === false ? 'policy-score' : 'personalized-pagerank+policy', preset: policy.preset, configSource: index?.memoryConfig?.source ?? 'default', weights: policy.weights, ppr: policy.ppr }, related, groups, omittedRelated: Math.max(0, relatedAll.length - related.length) };
+  return { changed: changedPaths[0], changedFiles: changedPaths, ranking: { method: policy.ppr.enabled === false ? 'policy-score' : 'personalized-pagerank+policy', preset: policy.preset, configSource: index?.memoryConfig?.source ?? 'default', weights: policy.weights, ppr: policy.ppr }, related, groups, omittedRelated: Math.max(0, relatedAll.length - related.length) };
+}
+
+export function buildImpactReport(index, changedPaths, limits = {}) {
+  const normalized = normalizeChangedPaths(changedPaths);
+  const aggregate = buildCombinedImpactReport(index, normalized, limits);
+  const perSeedLimit = limits.perSeed ?? 5;
+  aggregate.perSeed = normalized.map((changed) => {
+    const report = buildCombinedImpactReport(index, [changed], { ...limits, related: Math.max(limits.related ?? 25, perSeedLimit + 1) });
+    const related = report.related.filter((item) => item.id !== `file:${changed}`).slice(0, perSeedLimit);
+    return { changed, related, omittedRelated: Math.max(0, report.related.length - 1 - related.length) + report.omittedRelated };
+  });
+  return aggregate;
 }
 
 function compactScoreBreakdown(scoreBreakdown = {}) {
@@ -113,11 +132,14 @@ function compactImpactGroup(group = { items: [], omitted: 0 }, limit = 5) {
 }
 
 export function buildCompactImpactReport(impact, limits = {}) {
-  const relatedLimit = limits.related ?? 10;
+  const relatedLimit = Math.max(limits.related ?? 10, impact.changedFiles?.length ?? 1);
   const groupLimit = limits.groupItems ?? 5;
+  const changedFiles = impact.changedFiles ?? [impact.changed];
+  const seedIds = new Set(changedFiles.map((path) => `file:${path}`));
   const related = (impact.related ?? []).slice(0, relatedLimit).map(compactImpactItem);
   const groupNames = ['files', 'docs', 'contracts', 'tests', 'commands', 'events', 'packageResources', 'symbols'];
   const groups = Object.fromEntries(groupNames.map((name) => [name, compactImpactGroup(impact.groups?.[name], groupLimit)]));
-  const top10 = (impact.related ?? []).filter((item) => item.id !== `file:${impact.changed}`).slice(0, 10);
-  return { changed: impact.changed, compact: true, ranking: { method: impact.ranking?.method, preset: impact.ranking?.preset, configSource: impact.ranking?.configSource }, related, groups, omittedRelated: (impact.omittedRelated ?? 0) + Math.max(0, (impact.related?.length ?? 0) - related.length), quality: { rawRelated: impact.related?.length ?? 0, compactRelated: related.length, semanticOnlyTop10: top10.filter((item) => isSemanticOnlyImpactItem(item)).length, curatedTop10: top10.filter((item) => hasCuratedImpactReason(item)).length, lowActionabilityTop10: top10.filter((item) => isLowActionabilityImpactItem(item)).length } };
+  const perSeed = (impact.perSeed ?? []).map((entry) => ({ changed: entry.changed, related: (entry.related ?? []).slice(0, limits.perSeed ?? 5).map(compactImpactItem), omittedRelated: entry.omittedRelated ?? 0 }));
+  const top10 = (impact.related ?? []).filter((item) => !seedIds.has(item.id)).slice(0, 10);
+  return { changed: impact.changed, changedFiles, perSeed, compact: true, ranking: { method: impact.ranking?.method, preset: impact.ranking?.preset, configSource: impact.ranking?.configSource }, related, groups, omittedRelated: (impact.omittedRelated ?? 0) + Math.max(0, (impact.related?.length ?? 0) - related.length), quality: { rawRelated: impact.related?.length ?? 0, compactRelated: related.length, semanticOnlyTop10: top10.filter((item) => isSemanticOnlyImpactItem(item)).length, curatedTop10: top10.filter((item) => hasCuratedImpactReason(item)).length, lowActionabilityTop10: top10.filter((item) => isLowActionabilityImpactItem(item)).length } };
 }

package/src/impact/scoring.mjs

@@ -33,13 +33,16 @@ function cappedTraceabilityScore(reasons, boosts, cap) {
   return clamp(Math.max(...values) + Math.min(5, Math.max(0, values.length - 1) * 2), 0, cap);
 }
 
-export function buildPersonalizedPageRank(graph, seed, policy) {
+export function buildPersonalizedPageRank(graph, seeds, policy) {
   if (policy.ppr.enabled === false) return new Map();
+  const seedList = Array.isArray(seeds) ? [...new Set(seeds)] : [seeds];
+  const seedSet = new Set(seedList);
+  const restart = seedList.length > 0 ? 1 / seedList.length : 0;
   const damping = policy.ppr.damping ?? 0.85;
   const iterations = policy.ppr.iterations ?? 20;
   const tolerance = policy.ppr.tolerance ?? 0.000001;
   const ids = new Set(graph.nodes.map((node) => node.id));
-  ids.add(seed);
+  for (const seed of seedList) ids.add(seed);
   const adjacency = new Map([...ids].map((id) => [id, []]));
   for (const edge of graph.edges) {
     const weight = policy.relationWeights[edge.relation] ?? relationWeight(edge.relation);
@@ -49,9 +52,9 @@ export function buildPersonalizedPageRank(graph, seed, policy) {
     adjacency.get(edge.source).push([edge.target, weight]);
     adjacency.get(edge.target).push([edge.source, weight]);
   }
-  let ranks = new Map([...adjacency.keys()].map((id) => [id, id === seed ? 1 : 0]));
+  let ranks = new Map([...adjacency.keys()].map((id) => [id, seedSet.has(id) ? restart : 0]));
   for (let i = 0; i < iterations; i += 1) {
-    const next = new Map([...adjacency.keys()].map((id) => [id, id === seed ? 1 - damping : 0]));
+    const next = new Map([...adjacency.keys()].map((id) => [id, seedSet.has(id) ? (1 - damping) * restart : 0]));
     for (const [id, edges] of adjacency.entries()) {
       const rank = ranks.get(id) ?? 0;
       const total = edges.reduce((sum, [, weight]) => sum + weight, 0);
@@ -65,8 +68,10 @@ export function buildPersonalizedPageRank(graph, seed, policy) {
   return ranks;
 }
 
-export function scoreImpactItem(item, seed, changedPath, policy, pprScores, maxPpr) {
-  if (item.id === seed) return { impactScore: 100, scoreBreakdown: { seed: 100, ppr: 40, traceability: 0, memoryPolicy: 0, verification: 0, proximity: 0, semantic: 0, freshness: 0, archivePenalty: 0 } };
+export function scoreImpactItem(item, seeds, changedPaths, policy, pprScores, maxPpr) {
+  const seedSet = seeds instanceof Set ? seeds : new Set(Array.isArray(seeds) ? seeds : [seeds]);
+  const paths = Array.isArray(changedPaths) ? changedPaths : [changedPaths];
+  if (seedSet.has(item.id)) return { impactScore: 100, scoreBreakdown: { seed: 100, ppr: 40, traceability: 0, memoryPolicy: 0, verification: 0, proximity: 0, semantic: 0, freshness: 0, archivePenalty: 0 } };
   const reasons = item.reasons ?? [];
   const retrieval = item.retrieval ?? {};
   const pprNormalized = maxPpr > 0 ? (pprScores.get(item.id) ?? 0) / maxPpr : 0;
@@ -78,7 +83,7 @@ export function scoreImpactItem(item, seed, changedPath, policy, pprScores, maxP
   const semantic = clamp(sumReasonBoosts(reasons, policy.semanticBoosts), 0, Math.abs(policy.weights.semantic ?? 10));
   const freshness = retrieval.freshness === 'fresh' ? Math.abs(policy.weights.freshness ?? 5) : retrieval.freshness === 'stale' ? -Math.abs(policy.weights.freshness ?? 5) : 0;
   let archivePenalty = 0;
-  if (!changedPath.startsWith('docs/archive/')) {
+  if (!paths.some((path) => path.startsWith('docs/archive/'))) {
     if (retrieval.area === 'archive-body') archivePenalty -= Math.abs(policy.weights.archivePenalty ?? -25);
     if (retrieval.includeBodiesByDefault === false) archivePenalty -= 10;
     if (retrieval.freshness === 'stale' && retrieval.area !== 'archive-map') archivePenalty -= 5;
@@ -125,10 +130,17 @@ function impactSelectionScore(item) {
   return score;
 }
 
-export function compareImpactItems(seed) {
+export function compareImpactItems(seeds) {
+  const seedList = Array.isArray(seeds) ? seeds : [seeds];
+  const seedOrder = new Map(seedList.map((seed, index) => [seed, index]));
   return (a, b) => {
-    if (a.id === seed) return -1;
-    if (b.id === seed) return 1;
+    const aSeed = seedOrder.get(a.id);
+    const bSeed = seedOrder.get(b.id);
+    if (aSeed !== undefined || bSeed !== undefined) {
+      if (aSeed === undefined) return 1;
+      if (bSeed === undefined) return -1;
+      return aSeed - bSeed;
+    }
     return impactSelectionScore(b) - impactSelectionScore(a) || (b.impactScore ?? 0) - (a.impactScore ?? 0) || a.id.localeCompare(b.id);
   };
 }

package/src/init.mjs

@@ -1,5 +1,6 @@
 import { existsSync, mkdirSync, readFileSync, renameSync, statSync, writeFileSync } from 'node:fs';
 import { basename, dirname, join, resolve } from 'node:path';
+import { defaultDotdotgodConfigText } from './memory/config.mjs';
 
 function action(status, path, extra = {}) {
   return { status, path, ...extra };
@@ -9,6 +10,7 @@ function formatAction(item) {
   const extras = [];
   if (item.backup) extras.push(`backup=${item.backup}`);
   if (item.add) extras.push(`add=${item.add}`);
+  if (item.existing) extras.push(`existing=${item.existing}`);
   return `${item.status.padEnd(13)} ${item.path}${extras.length > 0 ? ` ${extras.join(' ')}` : ''}`;
 }
 
@@ -48,6 +50,14 @@ function initError(options, code, message) {
   process.exit(2);
 }
 
+function backupPathFor(target) {
+  const timestamp = new Date().toISOString().replace(/[-:]/g, '').replace(/\.\d{3}Z$/, 'Z');
+  const base = `${target}.bak.${timestamp}`;
+  let candidate = base;
+  for (let suffix = 1; existsSync(candidate); suffix += 1) candidate = `${base}.${suffix}`;
+  return candidate;
+}
+
 function writeInitFile(options, relativePath, content, actions) {
   const target = join(options.root, relativePath);
   if (existsSync(target) && !options.force) {
@@ -57,7 +67,7 @@ function writeInitFile(options, relativePath, content, actions) {
 
   let backup = '';
   if (existsSync(target) && options.force) {
-    backup = `${target}.bak.${new Date().toISOString().replace(/[-:]/g, '').replace(/\.\d{3}Z$/, 'Z')}`;
+    backup = backupPathFor(target);
     if (!options.dryRun) renameSync(target, backup);
   }
 
@@ -67,7 +77,7 @@ function writeInitFile(options, relativePath, content, actions) {
   }
 
   mkdirSync(dirname(target), { recursive: true });
-  writeFileSync(target, `${content}\n`);
+  writeFileSync(target, content.endsWith('\n') ? content : `${content}\n`);
   actions.push(action(backup ? 'replaced' : 'created', target, backup ? { backup } : {}));
 }
 
@@ -298,6 +308,12 @@ export function runInit(argv, usage) {
 
   const actions = [];
   for (const [relativePath, content] of initFiles(options)) writeInitFile(options, relativePath, content, actions);
+
+  const configPath = join(options.root, 'dotdotgod.config.json');
+  const rcPath = join(options.root, '.dotdotgodrc.json');
+  if (existsSync(rcPath)) actions.push(action('conflict', configPath, { existing: rcPath }));
+  else writeInitFile(options, 'dotdotgod.config.json', defaultDotdotgodConfigText(), actions);
+
   for (const entry of ['docs/plan', 'docs/archive', '.dotdotgod']) ensureGitignoreEntry(options, entry, actions);
 
   const payload = { ok: true, command: 'init', root: options.root, projectName: options.projectName, dryRun: options.dryRun, force: options.force, dotdotSetting: options.dotdotSetting, actions };