open-wiki-spec 0.2.3 → 0.3.0

package/dist/core/parser/wikilink-parser.js

@@ -9,18 +9,24 @@ export function extractWikilinks(text, location, startLine = 1) {
     const errors = [];
     const lines = text.split('\n');
     let insideCodeFence = false;
-    let codeFenceMarker = '';
+    let codeFenceMarker = ''; // The opening fence string (e.g., "```" or "~~~~~")
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i];
         const fenceMatch = line.match(CODE_FENCE_REGEX);
         if (fenceMatch) {
             if (!insideCodeFence) {
                 insideCodeFence = true;
-                codeFenceMarker = fenceMatch[1][0];
+                codeFenceMarker = fenceMatch[1]; // Store the full opening fence (e.g., "````")
             }
-            else if (line.trim().startsWith(codeFenceMarker.repeat(3))) {
-                insideCodeFence = false;
-                codeFenceMarker = '';
+            else {
+                // CommonMark: closing fence must have same marker char and length >= opening
+                const trimmed = line.trim();
+                const openChar = codeFenceMarker[0];
+                if (trimmed.length >= codeFenceMarker.length &&
+                    trimmed === openChar.repeat(trimmed.length)) {
+                    insideCodeFence = false;
+                    codeFenceMarker = '';
+                }
             }
             continue;
         }
@@ -41,6 +47,16 @@ export function extractWikilinks(text, location, startLine = 1) {
                 });
                 continue;
             }
+            // Warn on nested brackets (escaped delimiter is already split by regex, so only check brackets)
+            if (target.includes('[[') || target.includes(']]')) {
+                errors.push({
+                    level: 'warning',
+                    source: 'wikilink',
+                    message: `Malformed wikilink target with nested brackets or escaped delimiter: "${target}"`,
+                    line: startLine + i,
+                });
+                continue;
+            }
             // Strip #heading subpath (Obsidian [[Note#Heading]] syntax)
             const hashIndex = target.indexOf('#');
             const resolvedTarget = hashIndex !== -1 ? target.slice(0, hashIndex).trim() : target;

package/dist/core/parser/wikilink-parser.js.map

@@ -1 +1 @@
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+{"version":3,"file":"wikilink-parser.js","sourceRoot":"","sources":["../../../src/core/parser/wikilink-parser.ts"],"names":[],"mappings":"AAEA,MAAM,cAAc,GAAG,qCAAqC,CAAC;AAC7D,MAAM,gBAAgB,GAAG,gBAAgB,CAAC;AAE1C;;;GAGG;AACH,MAAM,UAAU,gBAAgB,CAC9B,IAAY,EACZ,QAAgC,EAChC,YAAoB,CAAC;IAErB,MAAM,SAAS,GAAyB,EAAE,CAAC;IAC3C,MAAM,MAAM,GAAiB,EAAE,CAAC;IAChC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;IAC/B,IAAI,eAAe,GAAG,KAAK,CAAC;IAC5B,IAAI,eAAe,GAAG,EAAE,CAAC,CAAE,oDAAoD;IAE/E,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QAEtB,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC;QAChD,IAAI,UAAU,EAAE,CAAC;YACf,IAAI,CAAC,eAAe,EAAE,CAAC;gBACrB,eAAe,GAAG,IAAI,CAAC;gBACvB,eAAe,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,8CAA8C;YACjF,CAAC;iBAAM,CAAC;gBACN,6EAA6E;gBAC7E,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;gBAC5B,MAAM,QAAQ,GAAG,eAAe,CAAC,CAAC,CAAC,CAAC;gBACpC,IAAI,OAAO,CAAC,MAAM,IAAI,eAAe,CAAC,MAAM;oBACxC,OAAO,KAAK,QAAQ,CAAC,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;oBAChD,eAAe,GAAG,KAAK,CAAC;oBACxB,eAAe,GAAG,EAAE,CAAC;gBACvB,CAAC;YACH,CAAC;YACD,SAAS;QACX,CAAC;QACD,IAAI,eAAe;YAAE,SAAS;QAE9B,kCAAkC;QAClC,MAAM,KAAK,GAAG,IAAI,MAAM,CAAC,cAAc,CAAC,MAAM,EAAE,cAAc,CAAC,KAAK,CAAC,CAAC;QACtE,IAAI,KAA6B,CAAC;QAElC,OAAO,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;YAC3C,MAAM,MAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YAC/B,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,IAAI,CAAC;YAEvC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACxB,MAAM,CAAC,IAAI,CAAC;oBACV,KAAK,EAAE,SAAS;oBAChB,MAAM,EAAE,UAAU;oBAClB,OAAO,EAAE,uBAAuB;oBAChC,IAAI,EAAE,SAAS,GAAG,CAAC;iBACpB,CAAC,CAAC;gBACH,SAAS;YACX,CAAC;YAED,gGAAgG;YAChG,IAAI,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;gBACnD,MAAM,CAAC,IAAI,CAAC;oBACV,KAAK,EAAE,SAAS;oBAChB,MAAM,EAAE,UAAU;oBAClB,OAAO,EAAE,yEAAyE,MAAM,GAAG;oBAC3F,IAAI,EAAE,SAAS,GAAG,CAAC;iBACpB,CAAC,CAAC;gBACH,SAAS;YACX,CAAC;YAED,4DAA4D;YAC5D,MAAM,SAAS,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;YACtC,MAAM,cAAc,GAAG,SAAS,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC;YAErF,IAAI,cAAc,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAChC,uDAAuD;gBACvD,SAAS;YACX,CAAC;YAED,SAAS,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,SAAS,GAAG,CAAC,EAAE,CAAC,CAAC;QACnF,CAAC;IACH,CAAC;IAED,OAAO,EAAE,SAAS,EAAE,MAAM,EAAE,CAAC;AAC/B,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,mBAAmB,CAAC,QAAgB;IAClD,IAAI,MAAM,GAAG,QAAQ,CAAC,IAAI,EAAE,CAAC;IAC7B,IAAI,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QACrD,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/B,CAAC;IACD,MAAM,SAAS,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;QACrB,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC;IACtC,CAAC;IACD,yBAAyB;IACzB,MAAM,SAAS,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;QACrB,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC;IACtC,CAAC;IACD,OAAO,MAAM,CAAC,IAAI,EAAE,CAAC;AACvB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB,CAAC,SAA+B;IACnE,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAC;IAClC,KAAK,MAAM,EAAE,IAAI,SAAS,EAAE,CAAC;QAC3B,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC;IACzB,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;AAC7B,CAAC"}

package/dist/core/retrieval/classify.d.ts

@@ -1,11 +1,18 @@
 import type { Classification, Confidence, ScoredCandidate, SequencingSummary } from '../../types/retrieval.js';
 import type { VaultIndex } from '../../types/index-record.js';
 import type { ClassificationThresholds } from './constants.js';
+export interface ClassifyDecision {
+    classification: Classification;
+    confidence: Confidence;
+    /** Human-readable justification — always present so downstream can display it. */
+    reason: string;
+}
 /**
  * Classify scored candidates using threshold rules (section 10.5).
+ * Every return path records a human-readable `reason` explaining which
+ * rule fired — this is what agents and `--json` consumers surface when
+ * the classification is `needs_confirmation` (so users know what to
+ * clarify) or when a `new_feature` default is picked silently.
  */
-export declare function classify(candidates: ScoredCandidate[], thresholds?: ClassificationThresholds, index?: VaultIndex, sequencing?: SequencingSummary): {
-    classification: Classification;
-    confidence: Confidence;
-};
+export declare function classify(rawCandidates: ScoredCandidate[], thresholds?: ClassificationThresholds, index?: VaultIndex, sequencing?: SequencingSummary): ClassifyDecision;
 //# sourceMappingURL=classify.d.ts.map

package/dist/core/retrieval/classify.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"classify.d.ts","sourceRoot":"","sources":["../../../src/core/retrieval/classify.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,UAAU,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAC/G,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAC9D,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAI/D,MAAM,WAAW,gBAAgB;IAC/B,cAAc,EAAE,cAAc,CAAC;IAC/B,UAAU,EAAE,UAAU,CAAC;IACvB,kFAAkF;IAClF,MAAM,EAAE,MAAM,CAAC;CAChB;AAED;;;;;;GAMG;AACH,wBAAgB,QAAQ,CACtB,aAAa,EAAE,eAAe,EAAE,EAChC,UAAU,GAAE,wBAA6C,EACzD,KAAK,CAAC,EAAE,UAAU,EAClB,UAAU,CAAC,EAAE,iBAAiB,GAC7B,gBAAgB,CA+KlB"}

package/dist/core/retrieval/classify.js

@@ -2,28 +2,58 @@ import { DEFAULT_THRESHOLDS } from './constants.js';
 import { isActiveChangeStatus } from './helpers.js';
 /**
  * Classify scored candidates using threshold rules (section 10.5).
+ * Every return path records a human-readable `reason` explaining which
+ * rule fired — this is what agents and `--json` consumers surface when
+ * the classification is `needs_confirmation` (so users know what to
+ * clarify) or when a `new_feature` default is picked silently.
  */
-export function classify(candidates, thresholds = DEFAULT_THRESHOLDS, index, sequencing) {
+export function classify(rawCandidates, thresholds = DEFAULT_THRESHOLDS, index, sequencing) {
+    // Dedupe by id up front. A scoring bug or an overly-enthusiastic graph
+    // expansion step could produce the same note twice in the candidate
+    // list; without dedup, `top`/`second` gap math gets confused (the gap
+    // is 0, incorrectly triggering `needs_confirmation`). Keep the first
+    // occurrence — scoring already sorts by score descending, so the
+    // first entry for any id is the highest-scored one.
+    const seen = new Set();
+    const candidates = [];
+    for (const c of rawCandidates) {
+        if (seen.has(c.id))
+            continue;
+        seen.add(c.id);
+        candidates.push(c);
+    }
     // Rule 0: Index-quality escalation
     if (index) {
         const topN = candidates.slice(0, 3);
         const topCandidatePaths = new Set(topN.map((c) => index.records.get(c.id)?.path).filter(Boolean));
-        const hasIndexQualityIssue = index.warnings.some((w) => (w.type === 'duplicate_id' ||
+        const qualityWarning = index.warnings.find((w) => (w.type === 'duplicate_id' ||
             w.type === 'ambiguous_alias' ||
             w.type === 'missing_id' ||
             w.type === 'unresolved_wikilink') &&
             topCandidatePaths.has(w.note_path));
-        if (hasIndexQualityIssue) {
-            return { classification: 'needs_confirmation', confidence: 'low' };
+        if (qualityWarning) {
+            return {
+                classification: 'needs_confirmation',
+                confidence: 'low',
+                reason: `Top candidate note has an index-quality issue (${qualityWarning.type}): ${qualityWarning.message}`,
+            };
         }
     }
     // Rule 0b: Sequencing severity escalation
     if (sequencing &&
         (sequencing.status === 'conflict_candidate' || sequencing.status === 'conflict_critical')) {
-        return { classification: 'needs_confirmation', confidence: 'low' };
+        return {
+            classification: 'needs_confirmation',
+            confidence: 'low',
+            reason: `Sequencing engine flagged status=${sequencing.status}: ${sequencing.reasons.join('; ') || 'active changes conflict with each other'}`,
+        };
     }
     if (candidates.length === 0) {
-        return { classification: 'new_feature', confidence: 'high' };
+        return {
+            classification: 'new_feature',
+            confidence: 'high',
+            reason: 'No matching notes in the vault — defaulting to new_feature.',
+        };
     }
     const top = candidates[0];
     const second = candidates.length > 1 ? candidates[1] : null;
@@ -33,7 +63,11 @@ export function classify(candidates, thresholds = DEFAULT_THRESHOLDS, index, seq
         isActiveChangeStatus(index?.records.get(top.id)?.status ?? '') &&
         top.score >= thresholds.existing_change.min_score &&
         gap >= thresholds.existing_change.min_gap_to_second) {
-        return { classification: 'existing_change', confidence: 'high' };
+        return {
+            classification: 'existing_change',
+            confidence: 'high',
+            reason: `Top candidate is an active Change "${top.title}" with score ${top.score} (gap to second = ${gap}).`,
+        };
     }
     // Rule 2: needs_confirmation (check before existing_feature)
     // Top two candidates >= 60 and gap < 10
@@ -41,7 +75,11 @@ export function classify(candidates, thresholds = DEFAULT_THRESHOLDS, index, seq
         top.score >= thresholds.needs_confirmation.min_top_two_score &&
         second.score >= thresholds.needs_confirmation.min_top_two_score &&
         gap < thresholds.needs_confirmation.max_score_gap) {
-        return { classification: 'needs_confirmation', confidence: 'low' };
+        return {
+            classification: 'needs_confirmation',
+            confidence: 'low',
+            reason: `Top two candidates both score high ("${top.title}"=${top.score}, "${second.title}"=${second.score}) with a small gap (${gap}); manual disambiguation needed.`,
+        };
     }
     // Feature and active Change both match strongly and conflict
     if (top.type === 'feature' &&
@@ -50,7 +88,11 @@ export function classify(candidates, thresholds = DEFAULT_THRESHOLDS, index, seq
         isActiveChangeStatus(index?.records.get(second.id)?.status ?? '') &&
         top.score >= thresholds.existing_feature.min_score &&
         second.score >= top.score - thresholds.existing_feature.max_active_change_gap) {
-        return { classification: 'needs_confirmation', confidence: 'low' };
+        return {
+            classification: 'needs_confirmation',
+            confidence: 'low',
+            reason: `Top candidate is Feature "${top.title}" (${top.score}) but active Change "${second.title}" (${second.score}) is close — should this change join the active one or target the Feature directly?`,
+        };
     }
     if (top.type === 'change' &&
         second &&
@@ -58,7 +100,11 @@ export function classify(candidates, thresholds = DEFAULT_THRESHOLDS, index, seq
         isActiveChangeStatus(index?.records.get(top.id)?.status ?? '') &&
         second.score >= thresholds.existing_feature.min_score &&
         top.score - second.score < thresholds.existing_feature.max_active_change_gap) {
-        return { classification: 'needs_confirmation', confidence: 'low' };
+        return {
+            classification: 'needs_confirmation',
+            confidence: 'low',
+            reason: `Top candidate is active Change "${top.title}" (${top.score}) but Feature "${second.title}" (${second.score}) is close — same ambiguity as above.`,
+        };
     }
     // Rule 3: existing_feature
     if (top.type === 'feature' && top.score >= thresholds.existing_feature.min_score) {
@@ -68,7 +114,11 @@ export function classify(candidates, thresholds = DEFAULT_THRESHOLDS, index, seq
             c.score >= top.score - thresholds.existing_feature.max_active_change_gap);
         if (!hasStrongActiveChange) {
             const confidence = top.score >= 85 ? 'high' : 'medium';
-            return { classification: 'existing_feature', confidence };
+            return {
+                classification: 'existing_feature',
+                confidence,
+                reason: `Top candidate is Feature "${top.title}" (${top.score}) with no competing active Change nearby.`,
+            };
         }
     }
     // Rule 4: new_feature
@@ -79,14 +129,26 @@ export function classify(candidates, thresholds = DEFAULT_THRESHOLDS, index, seq
     const topChangeScore = topChange?.score ?? 0;
     if (topFeatureScore < thresholds.new_feature.max_top_score &&
         topChangeScore < thresholds.new_feature.max_top_score) {
-        return { classification: 'new_feature', confidence: 'high' };
+        return {
+            classification: 'new_feature',
+            confidence: 'high',
+            reason: `Top Feature (${topFeatureScore}) and top Change (${topChangeScore}) are both below the new_feature threshold (${thresholds.new_feature.max_top_score}); nothing close enough to reuse.`,
+        };
     }
     // Fallback: ambiguous middle ground
     if (top.score >= thresholds.new_feature.max_top_score &&
         top.score < thresholds.existing_feature.min_score) {
-        return { classification: 'needs_confirmation', confidence: 'low' };
+        return {
+            classification: 'needs_confirmation',
+            confidence: 'low',
+            reason: `Top candidate "${top.title}" scores ${top.score}, in the ambiguous middle band (${thresholds.new_feature.max_top_score}-${thresholds.existing_feature.min_score}).`,
+        };
     }
     // Final fallback
-    return { classification: 'needs_confirmation', confidence: 'low' };
+    return {
+        classification: 'needs_confirmation',
+        confidence: 'low',
+        reason: 'No rule fired — retrieval produced candidates but none matched any clear classification branch.',
+    };
 }
 //# sourceMappingURL=classify.js.map

package/dist/core/retrieval/classify.js.map

@@ -1 +1 @@
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package/dist/core/retrieval/lexical.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lexical.d.ts","sourceRoot":"","sources":["../../../src/core/retrieval/lexical.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAC/D,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAE9D;;;GAGG;AACH,wBAAgB,gBAAgB,CAC9B,KAAK,EAAE,cAAc,EACrB,KAAK,EAAE,UAAU,GAChB,GAAG,CAAC,MAAM,CAAC,CA+Gb"}
+{"version":3,"file":"lexical.d.ts","sourceRoot":"","sources":["../../../src/core/retrieval/lexical.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAC/D,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAE9D;;;GAGG;AACH,wBAAgB,gBAAgB,CAC9B,KAAK,EAAE,cAAc,EACrB,KAAK,EAAE,UAAU,GAChB,GAAG,CAAC,MAAM,CAAC,CAmIb"}

package/dist/core/retrieval/lexical.js

@@ -8,6 +8,28 @@ export function lexicalRetrieval(query, index) {
     const searchTerms = allTerms.map((t) => t.toLowerCase());
     if (searchTerms.length === 0)
         return candidates;
+    // Precompute reverse indexes once: systemId → notes that list it, etc.
+    // Avoids O(n²) scanning during system/entity term matching.
+    const notesBySystem = new Map();
+    const notesBySource = new Map();
+    const notesByDecision = new Map();
+    for (const record of index.records.values()) {
+        for (const sysId of record.systems) {
+            const arr = notesBySystem.get(sysId) ?? [];
+            arr.push(record.id);
+            notesBySystem.set(sysId, arr);
+        }
+        for (const srcId of record.sources) {
+            const arr = notesBySource.get(srcId) ?? [];
+            arr.push(record.id);
+            notesBySource.set(srcId, arr);
+        }
+        for (const decId of record.decisions) {
+            const arr = notesByDecision.get(decId) ?? [];
+            arr.push(record.id);
+            notesByDecision.set(decId, arr);
+        }
+    }
     // 1. Title match
     for (const record of index.records.values()) {
         const titleLower = record.title.toLowerCase();
@@ -36,7 +58,7 @@ export function lexicalRetrieval(query, index) {
                 break;
         }
     }
-    // 3. System match
+    // 3. System match (uses precomputed notesBySystem reverse index)
     for (const term of query.system_terms) {
         const termLower = term.toLowerCase();
         for (const record of index.records.values()) {
@@ -44,11 +66,9 @@ export function lexicalRetrieval(query, index) {
                 if (record.title.toLowerCase().includes(termLower) ||
                     record.aliases.some((a) => a.toLowerCase().includes(termLower))) {
                     candidates.add(record.id);
-                    // Add all notes that list this system in their systems field
-                    for (const other of index.records.values()) {
-                        if (other.systems.includes(record.id)) {
-                            candidates.add(other.id);
-                        }
+                    const referencing = notesBySystem.get(record.id) ?? [];
+                    for (const otherId of referencing) {
+                        candidates.add(otherId);
                     }
                 }
             }
@@ -69,7 +89,7 @@ export function lexicalRetrieval(query, index) {
             }
         }
     }
-    // 5. Source / Decision match
+    // 5. Source / Decision match (uses precomputed notesBySource/notesByDecision reverse indexes)
     for (const term of query.entity_terms) {
         const termLower = term.toLowerCase();
         for (const record of index.records.values()) {
@@ -77,11 +97,10 @@ export function lexicalRetrieval(query, index) {
                 if (record.title.toLowerCase().includes(termLower) ||
                     record.aliases.some((a) => a.toLowerCase().includes(termLower))) {
                     candidates.add(record.id);
-                    // Include notes that reference this source/decision
-                    for (const other of index.records.values()) {
-                        if (other.sources.includes(record.id) || other.decisions.includes(record.id)) {
-                            candidates.add(other.id);
-                        }
+                    const refByType = record.type === 'source' ? notesBySource : notesByDecision;
+                    const referencing = refByType.get(record.id) ?? [];
+                    for (const otherId of referencing) {
+                        candidates.add(otherId);
                     }
                 }
             }

package/dist/core/retrieval/lexical.js.map

@@ -1 +1 @@
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+{"version":3,"file":"lexical.js","sourceRoot":"","sources":["../../../src/core/retrieval/lexical.ts"],"names":[],"mappings":"AAGA;;;GAGG;AACH,MAAM,UAAU,gBAAgB,CAC9B,KAAqB,EACrB,KAAiB;IAEjB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAU,CAAC;IACrC,MAAM,QAAQ,GAAG,CAAC,GAAG,KAAK,CAAC,aAAa,EAAE,GAAG,KAAK,CAAC,YAAY,EAAE,GAAG,KAAK,CAAC,YAAY,CAAC,CAAC;IACxF,MAAM,WAAW,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;IAEzD,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,UAAU,CAAC;IAEhD,uEAAuE;IACvE,4DAA4D;IAC5D,MAAM,aAAa,GAAG,IAAI,GAAG,EAAoB,CAAC;IAClD,MAAM,aAAa,GAAG,IAAI,GAAG,EAAoB,CAAC;IAClD,MAAM,eAAe,GAAG,IAAI,GAAG,EAAoB,CAAC;IACpD,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;QAC5C,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YACnC,MAAM,GAAG,GAAG,aAAa,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC3C,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;YACpB,aAAa,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;QAChC,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YACnC,MAAM,GAAG,GAAG,aAAa,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC3C,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;YACpB,aAAa,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;QAChC,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,MAAM,GAAG,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC7C,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;YACpB,eAAe,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;IAED,iBAAiB;IACjB,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;QAC5C,MAAM,UAAU,GAAG,MAAM,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC;QAC9C,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;YAC/B,IAAI,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;gBAC9B,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;gBAC1B,MAAM;YACR,CAAC;QACH,CAAC;IACH,CAAC;IAED,iBAAiB;IACjB,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;QAC5C,IAAI,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;YAAE,SAAS;QACxC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YACnC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;YACvC,IAAI,KAAK,GAAG,KAAK,CAAC;YAClB,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;gBAC/B,IAAI,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;oBAC9B,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;oBAC1B,KAAK,GAAG,IAAI,CAAC;oBACb,MAAM;gBACR,CAAC;YACH,CAAC;YACD,IAAI,KAAK;gBAAE,MAAM;QACnB,CAAC;IACH,CAAC;IAED,iEAAiE;IACjE,KAAK,MAAM,IAAI,IAAI,KAAK,CAAC,YAAY,EAAE,CAAC;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;QACrC,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;YAC5C,IAAI,MAAM,CAAC,IAAI,KAAK,QAAQ,EAAE,CAAC;gBAC7B,IACE,MAAM,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC;oBAC9C,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,EAC/D,CAAC;oBACD,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;oBAC1B,MAAM,WAAW,GAAG,aAAa,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,EAAE,CAAC;oBACvD,KAAK,MAAM,OAAO,IAAI,WAAW,EAAE,CAAC;wBAClC,UAAU,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;oBAC1B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,wBAAwB;IACxB,MAAM,iBAAiB,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,MAAM,CAC9C,CAAC,EAAE,EAAE,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,KAAK,SAAS,CAClD,CAAC;IACF,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;QAC5C,IAAI,MAAM,CAAC,IAAI,KAAK,QAAQ,EAAE,CAAC;YAC7B,MAAM,aAAa,GAAG,MAAM,CAAC,OAAO,IAAI,IAAI,CAAC;YAC7C,MAAM,cAAc,GAAG,MAAM,CAAC,QAAQ,IAAI,EAAE,CAAC;YAC7C,MAAM,UAAU,GAAG,aAAa,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC;YACvF,KAAK,MAAM,GAAG,IAAI,iBAAiB,EAAE,CAAC;gBACpC,IAAI,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC7B,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;oBAC1B,MAAM;gBACR,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,8FAA8F;IAC9F,KAAK,MAAM,IAAI,IAAI,KAAK,CAAC,YAAY,EAAE,CAAC;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;QACrC,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;YAC5C,IAAI,MAAM,CAAC,IAAI,KAAK,QAAQ,IAAI,MAAM,CAAC,IAAI,KAAK,UAAU,EAAE,CAAC;gBAC3D,IACE,MAAM,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC;oBAC9C,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,EAC/D,CAAC;oBACD,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;oBAC1B,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,eAAe,CAAC;oBAC7E,MAAM,WAAW,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,EAAE,CAAC;oBACnD,KAAK,MAAM,OAAO,IAAI,WAAW,EAAE,CAAC;wBAClC,UAAU,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;oBAC1B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,qBAAqB;IACrB,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;QAC5C,IAAI,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;YAAE,SAAS;QACxC,MAAM,SAAS,GAAG,MAAM,CAAC,QAAQ,CAAC,WAAW,EAAE,CAAC;QAChD,IAAI,UAAU,GAAG,CAAC,CAAC;QACnB,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;YAC/B,IAAI,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;gBAC7B,UAAU,EAAE,CAAC;YACf,CAAC;QACH,CAAC;QACD,IAAI,UAAU,IAAI,CAAC,IAAI,CAAC,UAAU,IAAI,CAAC,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;YACrE,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QAC5B,CAAC;IACH,CAAC;IAED,OAAO,UAAU,CAAC;AACpB,CAAC"}

package/dist/core/retrieval/retrieve.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"retrieve.d.ts","sourceRoot":"","sources":["../../../src/core/retrieval/retrieve.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAqB,MAAM,0BAA0B,CAAC;AACnG,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAC9D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAC;AAClE,OAAO,KAAK,EAAE,cAAc,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAS/E,MAAM,WAAW,gBAAgB;IAC/B,OAAO,CAAC,EAAE,OAAO,CAAC,cAAc,CAAC,CAAC;IAClC,UAAU,CAAC,EAAE,OAAO,CAAC,wBAAwB,CAAC,CAAC;IAC/C,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B;;;;OAIG;IACH,cAAc,CAAC,EAAE,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC9C;AAuBD;;;GAGG;AACH,wBAAgB,QAAQ,CACtB,KAAK,EAAE,UAAU,EACjB,KAAK,EAAE,cAAc,EACrB,OAAO,CAAC,EAAE,gBAAgB,GACzB,eAAe,CAwDjB"}
+{"version":3,"file":"retrieve.d.ts","sourceRoot":"","sources":["../../../src/core/retrieval/retrieve.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAqB,MAAM,0BAA0B,CAAC;AACnG,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAC9D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAC;AAClE,OAAO,KAAK,EAAE,cAAc,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAS/E,MAAM,WAAW,gBAAgB;IAC/B,OAAO,CAAC,EAAE,OAAO,CAAC,cAAc,CAAC,CAAC;IAClC,UAAU,CAAC,EAAE,OAAO,CAAC,wBAAwB,CAAC,CAAC;IAC/C,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B;;;;OAIG;IACH,cAAc,CAAC,EAAE,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC9C;AAuBD;;;GAGG;AACH,wBAAgB,QAAQ,CACtB,KAAK,EAAE,UAAU,EACjB,KAAK,EAAE,cAAc,EACrB,OAAO,CAAC,EAAE,gBAAgB,GACzB,eAAe,CAgGjB"}

package/dist/core/retrieval/retrieve.js

@@ -32,6 +32,7 @@ export function retrieve(index, query, options) {
     const lexicalCandidates = lexicalRetrieval(query, index);
     // Step 1b: Merge semantic candidates (if available) before graph expansion
     const semanticScores = options?.semanticScores;
+    const semanticUsed = semanticScores !== undefined && semanticScores.size > 0;
     const firstPass = new Set(lexicalCandidates);
     if (semanticScores) {
         for (const id of semanticScores.keys()) {
@@ -47,25 +48,64 @@ export function retrieve(index, query, options) {
         ? new Map(semanticScores)
         : undefined;
     const scored = scoreCandidates(expanded, query, index, weights, embeddingScores);
+    // Step 3b: Filter out Query notes for non-query intents. Query notes
+    // store investigation history — they share terms with whatever
+    // feature they were written about, so lexical retrieval happily
+    // surfaces them as top candidates when a user later proposes a
+    // related change. That pollutes classification (a past Query note
+    // shouldn't win against the actual Feature it investigated). Keep
+    // them only when the caller explicitly asked for them via
+    // intent='query' (the `ows query` workflow path).
+    const filteredScored = query.intent === 'query'
+        ? scored
+        : scored.filter((c) => c.type !== 'query');
     // Trim to max candidates
-    const topCandidates = scored.slice(0, maxCandidates);
+    const topCandidates = filteredScored.slice(0, maxCandidates);
     // Step 4: Classify
     const sequencingFull = options?.sequencing ?? null;
     const sequencingSummary = sequencingFull
         ? summarizeForRetrieval(sequencingFull)
         : { status: 'parallel_safe', related_changes: [], reasons: [] };
-    const { classification, confidence } = classify(topCandidates, thresholds, index, sequencingSummary);
-    // Step 5: Warnings
+    // Step 4a: Guard against under-specified queries.
+    // If normalization dropped every token (e.g., the user typed only stop
+    // words like "the and is", or pasted punctuation), both term arrays and
+    // the candidate set will be empty. The default classify() rule then
+    // returns `new_feature / high` — which causes `propose` to confidently
+    // create a brand-new Feature/Change pair from essentially no signal.
+    // That is the worst possible default: silent, irreversible, and
+    // high-confidence wrong. Short-circuit to `needs_confirmation` with a
+    // clear warning so the user is prompted to rephrase.
+    const hasAnyTerms = query.feature_terms.length > 0 ||
+        query.system_terms.length > 0 ||
+        query.entity_terms.length > 0;
     const internalWarnings = collectWarnings(index, topCandidates);
     const warnings = internalWarnings.map((w) => w.message);
+    if (!hasAnyTerms && topCandidates.length === 0) {
+        const underSpecifiedReason = 'Query is under-specified: no meaningful search terms were extracted. ' +
+            'Rephrase with concrete nouns or verbs.';
+        warnings.unshift(underSpecifiedReason);
+        return {
+            query: query.summary,
+            classification: 'needs_confirmation',
+            confidence: 'low',
+            sequencing: sequencingSummary,
+            candidates: topCandidates,
+            warnings,
+            classification_reason: underSpecifiedReason,
+            semantic_used: semanticUsed,
+        };
+    }
+    const decision = classify(topCandidates, thresholds, index, sequencingSummary);
     // Step 6: Assemble
     return {
         query: query.summary,
-        classification,
-        confidence,
+        classification: decision.classification,
+        confidence: decision.confidence,
         sequencing: sequencingSummary,
         candidates: topCandidates,
         warnings,
+        classification_reason: decision.reason,
+        semantic_used: semanticUsed,
     };
 }
 //# sourceMappingURL=retrieve.js.map

package/dist/core/retrieval/retrieve.js.map

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package/dist/core/retrieval/scoring.d.ts.map

@@ -1 +1 @@
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package/dist/core/retrieval/scoring.js

@@ -13,6 +13,13 @@ export function scoreCandidates(candidateIds, query, index, weights = DEFAULT_WE
         const record = index.records.get(id);
         if (!record)
             continue;
+        // Exclude archived changes from active retrieval unless the record type
+        // is not a change (Feature/System/Decision/Source/Query can be archived
+        // but shouldn't be filtered out just because a change references them).
+        // The path-based check catches notes physically located in 99-archive/.
+        if (record.type === 'change' && record.path.includes('99-archive/')) {
+            continue;
+        }
         const signals = [];
         // Signal 1: Title match (exact, prefix-stripped, or partial)
         const titleLower = record.title.toLowerCase();
@@ -40,9 +47,14 @@ export function scoreCandidates(candidateIds, query, index, weights = DEFAULT_WE
                 reason: `partial title match: "${record.title}"`,
             });
         }
-        // Signal 2: Alias match (at most once)
+        // Signal 2: Alias match (at most once, skip if alias duplicates the title match)
+        const titleAlreadyMatched = signals.some((s) => s.signal === 'exact_title');
         for (const alias of record.aliases) {
             const aliasLower = alias.toLowerCase();
+            // Skip alias if it's the same as the title or prefix-stripped title (avoids double-counting)
+            if (titleAlreadyMatched && (aliasLower === titleLower || aliasLower === titleWithoutPrefix)) {
+                continue;
+            }
             if (searchTerms.some((t) => aliasLower.includes(t))) {
                 signals.push({
                     signal: 'alias_match',
@@ -173,23 +185,36 @@ export function scoreCandidates(candidateIds, query, index, weights = DEFAULT_WE
         }
         // Signal 10: Semantic similarity (embedding-based, section 9.2)
         if (embeddingScores && weights.semantic_similarity) {
-            const similarity = embeddingScores.get(id);
-            if (similarity !== undefined && similarity > 0.7) {
-                const points = Math.round(similarity * weights.semantic_similarity);
-                signals.push({
-                    signal: 'semantic_similarity',
-                    points,
-                    reason: `semantic match: ${similarity.toFixed(2)}`,
-                });
+            const rawSimilarity = embeddingScores.get(id);
+            // Guard against NaN/Infinity and out-of-range values polluting the
+            // score. Cosine similarity should be in [0, 1] for normalized
+            // vectors, but corrupt cache entries or unusual embedder outputs
+            // can produce values > 1 or < 0. Clamp to [0, 1] so a bad score
+            // cannot overwhelm lexical signals and distort classification.
+            if (typeof rawSimilarity === 'number' &&
+                Number.isFinite(rawSimilarity) &&
+                Number.isFinite(weights.semantic_similarity)) {
+                const similarity = Math.max(0, Math.min(1, rawSimilarity));
+                if (similarity > 0.7) {
+                    const points = Math.round(similarity * weights.semantic_similarity);
+                    if (Number.isFinite(points)) {
+                        signals.push({
+                            signal: 'semantic_similarity',
+                            points,
+                            reason: `semantic match: ${similarity.toFixed(2)}`,
+                        });
+                    }
+                }
             }
         }
-        // Compute total score
-        let totalScore = signals.reduce((sum, s) => sum + s.points, 0);
+        // Compute total score — filter any non-finite signals before summing so
+        // one bad weight cannot poison the whole record's score.
+        let totalScore = signals.reduce((sum, s) => (Number.isFinite(s.points) ? sum + s.points : sum), 0);
         // Status bias bonus (minor tiebreaker)
         if (query.status_bias.includes(record.status)) {
             totalScore += 5;
         }
-        if (totalScore > 0) {
+        if (Number.isFinite(totalScore) && totalScore > 0) {
             scored.push({
                 id: record.id,
                 type: record.type,

package/dist/core/retrieval/scoring.js.map

@@ -1 +1 @@
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