open-wiki-spec 0.2.4 → 0.3.0

package/dist/core/migrate/spec-converter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"spec-converter.js","sourceRoot":"","sources":["../../../src/core/migrate/spec-converter.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,mBAAmB,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,eAAe,CAAC;AAEpF,MAAM,sBAAsB,GAAG,6BAA6B,CAAC;AAC7D,MAAM,mBAAmB,GAAG,2BAA2B,CAAC;AACxD,MAAM,kBAAkB,GAAG,iBAAiB,CAAC;AAC7C,MAAM,uBAAuB,GAAG,sBAAsB,CAAC;AACvD,MAAM,cAAc,GAAG,aAAa,CAAC;AAErC;;GAEG;AACH,MAAM,UAAU,WAAW,CAAC,IAAiB,EAAE,SAAiB;IAC9D,MAAM,EAAE,GAAG,mBAAmB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IAChD,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IAC3C,MAAM,OAAO,GAAG,cAAc,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IAC7C,MAAM,iBAAiB,GAAG,wBAAwB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACjE,MAAM,WAAW,GAAG,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACrD,MAAM,SAAS,GAAG,gBAAgB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IAEjD,MAAM,OAAO,GAAG,gBAAgB,CAAC;QAC/B,EAAE;QACF,KAAK;QACL,SAAS;QACT,OAAO;QACP,iBAAiB;QACjB,WAAW;QACX,SAAS;KACV,CAAC,CAAC;IAEH,OAAO;QACL,UAAU,EAAE,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,aAAa,EAAE,GAAG,EAAE,KAAK,CAAC;QACxD,OAAO;QACP,iBAAiB,EAAE,kBAAkB,IAAI,CAAC,UAAU,UAAU;KAC/D,CAAC;AACJ,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,eAAe,CAC7B,KAAoB,EACpB,UAA+B;IAE/B,MAAM,OAAO,GAAuB,EAAE,CAAC;IACvC,MAAM,QAAQ,GAAa,EAAE,CAAC;IAE9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,SAAS,GAAG,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,IAAI,gBAAgB,CAAC;QACtE,IAAI,CAAC;YACH,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC;QAC7C,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,QAAQ,CAAC,IAAI,CAAC,0BAA0B,IAAI,CAAC,UAAU,KAAM,GAAa,CAAC,OAAO,EAAE,CAAC,CAAC;QACxF,CAAC;IACH,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAC;AAC/B,CAAC;AAED,SAAS,gBAAgB,CAAC,IAQzB;IACC,OAAO;;MAEH,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;;;MAGvB,cAAc,CAAC,IAAI,CAAC,SAAS,CAAC;;;;;;;;;aASvB,IAAI,CAAC,KAAK;;;;EAIrB,IAAI,CAAC,OAAO,IAAI,yDAAyD;;;;;;;;EAQzE,IAAI,CAAC,WAAW,IAAI,oDAAoD;;;;EAIxE,IAAI,CAAC,SAAS,IAAI,mDAAmD;;;;EAIrE,IAAI,CAAC,iBAAiB,IAAI,iDAAiD;;;;;;;;CAQ5E,CAAC;AACF,CAAC;AAED;;GAEG;AACH,SAAS,cAAc,CAAC,OAAe;IACrC,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC;IAChD,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,+CAA+C;QAC/C,MAAM,KAAK,GAAG,OAAO,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QACvC,IAAI,KAAK,KAAK,CAAC,CAAC;YAAE,OAAO,EAAE,CAAC;QAC5B,MAAM,OAAO,GAAG,OAAO,CAAC,KAAK,CAAC,gCAAgC,CAAC,CAAC;QAChE,IAAI,OAAO;YAAE,OAAO,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;QACtC,OAAO,EAAE,CAAC;IACZ,CAAC;IAED,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IAChD,MAAM,WAAW,GAAG,OAAO,CAAC,OAAO,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACvD,MAAM,cAAc,GAAG,WAAW,KAAK,CAAC,CAAC;QACvC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC;QACzB,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAC;IAEzC,OAAO,cAAc,CAAC,IAAI,EAAE,CAAC;AAC/B,CAAC;AAED;;GAEG;AACH,SAAS,wBAAwB,CAAC,OAAe;IAC/C,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAC;IACrD,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IAEtB,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IAChD,yEAAyE;IACzE,MAAM,SAAS,GAAG,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;IAC1C,MAAM,MAAM,GAAG,SAAS,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAC;IACxD,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,KAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;IAErE,OAAO,KAAK,CAAC,IAAI,EAAE,CAAC;AACtB,CAAC;AAED;;GAEG;AACH,SAAS,kBAAkB,CAAC,OAAe;IACzC,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAC;IACnD,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IAChD,MAAM,WAAW,GAAG,OAAO,CAAC,OAAO,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACvD,OAAO,CAAC,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;AACtG,CAAC;AAED;;GAEG;AACH,SAAS,gBAAgB,CAAC,OAAe;IACvC,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,sBAAsB,CAAC,CAAC;IACpD,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IAChD,MAAM,WAAW,GAAG,OAAO,CAAC,OAAO,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACvD,OAAO,CAAC,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;AACtG,CAAC;AAED;;GAEG;AACH,SAAS,WAAW,CAAC,UAAkB;IACrC,OAAO,UAAU;SACd,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;SACzD,IAAI,CAAC,GAAG,CAAC,CAAC;AACf,CAAC"}

package/dist/core/migrate/types.d.ts

@@ -121,5 +121,14 @@ export interface MigrateOptions {
     skipArchive?: boolean;
     /** Output as JSON */
     json?: boolean;
+    /**
+     * Allow migration to proceed even when a `wiki/` directory with typed
+     * notes already exists at the target path. Without this flag, migrate
+     * refuses so the user doesn't silently interleave an openspec import
+     * into an already-bootstrapped vault — which causes half-merged state
+     * that only surfaces later as `filesSkipped` entries and unresolved
+     * wikilinks. Setting this flag acknowledges the risk explicitly.
+     */
+    allowExistingVault?: boolean;
 }
 //# sourceMappingURL=types.d.ts.map

package/dist/core/migrate/types.d.ts.map

@@ -1 +1 @@
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package/dist/core/parser/frontmatter-parser.d.ts

@@ -1,11 +1,5 @@
 import { type Frontmatter } from '../schema/frontmatter.js';
 import type { RawFrontmatter, ParseError } from './types.js';
-/**
- * Extract YAML frontmatter from a markdown string.
- *
- * Frontmatter is delimited by --- on its own line at the start of the file
- * and a closing --- on its own line.
- */
 export declare function extractFrontmatter(content: string): {
     raw: RawFrontmatter | null;
     errors: ParseError[];

package/dist/core/parser/frontmatter-parser.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"frontmatter-parser.d.ts","sourceRoot":"","sources":["../../../src/core/parser/frontmatter-parser.ts"],"names":[],"mappings":"AACA,OAAO,EAAqB,KAAK,WAAW,EAAE,MAAM,0BAA0B,CAAC;AAC/E,OAAO,KAAK,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,YAAY,CAAC;AAe7D,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,MAAM,GAAG;IAAE,GAAG,EAAE,cAAc,GAAG,IAAI,CAAC;IAAC,MAAM,EAAE,UAAU,EAAE,CAAA;CAAE,CA8ExG;AAED;;;GAGG;AACH,wBAAgB,mBAAmB,CACjC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC5B;IAAE,WAAW,EAAE,WAAW,GAAG,IAAI,CAAC;IAAC,MAAM,EAAE,UAAU,EAAE,CAAA;CAAE,CAwD3D"}

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

@@ -6,9 +6,17 @@ import { FrontmatterSchema } from '../schema/frontmatter.js';
  * Frontmatter is delimited by --- on its own line at the start of the file
  * and a closing --- on its own line.
  */
+/**
+ * Maximum size (in bytes) of the YAML frontmatter block.
+ * Guards against pathological inputs (e.g., multi-MB YAML) that could
+ * cause excessive memory use or parser slowdown.
+ */
+const MAX_FRONTMATTER_SIZE = 1024 * 1024; // 1 MiB
 export function extractFrontmatter(content) {
     const errors = [];
-    const normalized = content.replace(/\r\n/g, '\n').replace(/\r/g, '\n');
+    // Strip UTF-8 BOM if present (some editors like Windows Notepad add it)
+    const stripped = content.charCodeAt(0) === 0xFEFF ? content.slice(1) : content;
+    const normalized = stripped.replace(/\r\n/g, '\n').replace(/\r/g, '\n');
     const lines = normalized.split('\n');
     if (lines.length === 0 || lines[0].trim() !== '---') {
         errors.push({
@@ -19,9 +27,11 @@ export function extractFrontmatter(content) {
         });
         return { raw: null, errors };
     }
+    // Find closing delimiter: must be `---` at column 0 (not indented).
+    // Indented `---` inside block scalars (e.g., `summary: |`) must not be treated as a delimiter.
     let closeIndex = -1;
     for (let i = 1; i < lines.length; i++) {
-        if (lines[i].trim() === '---') {
+        if (lines[i] === '---' || lines[i] === '--- ') {
             closeIndex = i;
             break;
         }
@@ -38,6 +48,16 @@ export function extractFrontmatter(content) {
     const yamlContent = lines.slice(1, closeIndex).join('\n');
     const body = lines.slice(closeIndex + 1).join('\n');
     const bodyStartLine = closeIndex + 2; // 1-indexed, line after closing ---
+    // Guard against pathological YAML sizes
+    if (yamlContent.length > MAX_FRONTMATTER_SIZE) {
+        errors.push({
+            level: 'error',
+            source: 'frontmatter',
+            message: `Frontmatter exceeds ${MAX_FRONTMATTER_SIZE} bytes (got ${yamlContent.length}). Refusing to parse.`,
+            line: 1,
+        });
+        return { raw: null, errors };
+    }
     let data;
     try {
         data = parseYaml(yamlContent);
@@ -71,6 +91,43 @@ export function extractFrontmatter(content) {
  */
 export function validateFrontmatter(data) {
     const errors = [];
+    // Detect `key: null` for fields that must be arrays. YAML authors often
+    // write `aliases:` (empty value → null) or `tags: null` expecting an
+    // empty list, but the schema's passthrough() silently accepts null and
+    // downstream `getArray()` coerces it to []. Surface the ambiguity as a
+    // warning so the user can fix it explicitly.
+    const ARRAY_FIELDS = ['aliases', 'tags', 'systems', 'sources', 'decisions', 'changes', 'depends_on', 'touches', 'features'];
+    for (const field of ARRAY_FIELDS) {
+        if (field in data && data[field] === null) {
+            errors.push({
+                level: 'warning',
+                source: 'frontmatter',
+                message: `Frontmatter field "${field}" is null. Use an empty list "[]" or omit the field instead. Treating as empty list.`,
+            });
+            // Normalize to empty array so downstream consumers get a predictable shape.
+            data[field] = [];
+        }
+    }
+    // Detect case-variant reserved keys (e.g., "Type" instead of "type") and
+    // give a clear, actionable error. YAML is case-sensitive, so these would
+    // otherwise fail Zod validation with a confusing "missing required" error.
+    const reservedKeys = ['type', 'id', 'status', 'tags'];
+    const dataKeys = Object.keys(data);
+    for (const reserved of reservedKeys) {
+        if (!(reserved in data)) {
+            const variant = dataKeys.find((k) => k !== reserved && k.toLowerCase() === reserved);
+            if (variant) {
+                errors.push({
+                    level: 'error',
+                    source: 'frontmatter',
+                    message: `Frontmatter key "${variant}" must be lowercase "${reserved}". YAML keys are case-sensitive.`,
+                });
+            }
+        }
+    }
+    if (errors.length > 0) {
+        return { frontmatter: null, errors };
+    }
     const result = FrontmatterSchema.safeParse(data);
     if (!result.success) {
         for (const issue of result.error.issues) {

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

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+{"version":3,"file":"frontmatter-parser.js","sourceRoot":"","sources":["../../../src/core/parser/frontmatter-parser.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,IAAI,SAAS,EAAE,MAAM,MAAM,CAAC;AAC1C,OAAO,EAAE,iBAAiB,EAAoB,MAAM,0BAA0B,CAAC;AAG/E;;;;;GAKG;AACH;;;;GAIG;AACH,MAAM,oBAAoB,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,QAAQ;AAElD,MAAM,UAAU,kBAAkB,CAAC,OAAe;IAChD,MAAM,MAAM,GAAiB,EAAE,CAAC;IAChC,wEAAwE;IACxE,MAAM,QAAQ,GAAG,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;IAC/E,MAAM,UAAU,GAAG,QAAQ,CAAC,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC;IACxE,MAAM,KAAK,GAAG,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;IAErC,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,KAAK,EAAE,CAAC;QACpD,MAAM,CAAC,IAAI,CAAC;YACV,KAAK,EAAE,OAAO;YACd,MAAM,EAAE,aAAa;YACrB,OAAO,EAAE,2DAA2D;YACpE,IAAI,EAAE,CAAC;SACR,CAAC,CAAC;QACH,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;IAC/B,CAAC;IAED,oEAAoE;IACpE,+FAA+F;IAC/F,IAAI,UAAU,GAAG,CAAC,CAAC,CAAC;IACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,KAAK,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,MAAM,EAAE,CAAC;YAC9C,UAAU,GAAG,CAAC,CAAC;YACf,MAAM;QACR,CAAC;IACH,CAAC;IAED,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;QACtB,MAAM,CAAC,IAAI,CAAC;YACV,KAAK,EAAE,OAAO;YACd,MAAM,EAAE,aAAa;YACrB,OAAO,EAAE,8CAA8C;YACvD,IAAI,EAAE,CAAC;SACR,CAAC,CAAC;QACH,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;IAC/B,CAAC;IAED,MAAM,WAAW,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC1D,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACpD,MAAM,aAAa,GAAG,UAAU,GAAG,CAAC,CAAC,CAAC,oCAAoC;IAE1E,wCAAwC;IACxC,IAAI,WAAW,CAAC,MAAM,GAAG,oBAAoB,EAAE,CAAC;QAC9C,MAAM,CAAC,IAAI,CAAC;YACV,KAAK,EAAE,OAAO;YACd,MAAM,EAAE,aAAa;YACrB,OAAO,EAAE,uBAAuB,oBAAoB,eAAe,WAAW,CAAC,MAAM,uBAAuB;YAC5G,IAAI,EAAE,CAAC;SACR,CAAC,CAAC;QACH,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;IAC/B,CAAC;IAED,IAAI,IAA6B,CAAC;IAClC,IAAI,CAAC;QACH,IAAI,GAAG,SAAS,CAAC,WAAW,CAAC,CAAC;QAC9B,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,IAAI,KAAK,IAAI,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACrE,MAAM,CAAC,IAAI,CAAC;gBACV,KAAK,EAAE,OAAO;gBACd,MAAM,EAAE,aAAa;gBACrB,OAAO,EAAE,sDAAsD;gBAC/D,IAAI,EAAE,CAAC;aACR,CAAC,CAAC;YACH,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;QAC/B,CAAC;IACH,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,CAAC,IAAI,CAAC;YACV,KAAK,EAAE,OAAO;YACd,MAAM,EAAE,aAAa;YACrB,OAAO,EAAE,gCAAiC,CAAW,CAAC,OAAO,EAAE;YAC/D,IAAI,EAAE,CAAC;SACR,CAAC,CAAC;QACH,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;IAC/B,CAAC;IAED,OAAO;QACL,GAAG,EAAE,EAAE,IAAI,EAAE,IAA+B,EAAE,IAAI,EAAE,aAAa,EAAE;QACnE,MAAM;KACP,CAAC;AACJ,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAA6B;IAE7B,MAAM,MAAM,GAAiB,EAAE,CAAC;IAEhC,wEAAwE;IACxE,qEAAqE;IACrE,uEAAuE;IACvE,uEAAuE;IACvE,6CAA6C;IAC7C,MAAM,YAAY,GAAG,CAAC,SAAS,EAAE,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,WAAW,EAAE,SAAS,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,CAAC,CAAC;IAC5H,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;QACjC,IAAI,KAAK,IAAI,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,EAAE,CAAC;YAC1C,MAAM,CAAC,IAAI,CAAC;gBACV,KAAK,EAAE,SAAS;gBAChB,MAAM,EAAE,aAAa;gBACrB,OAAO,EAAE,sBAAsB,KAAK,sFAAsF;aAC3H,CAAC,CAAC;YACH,4EAA4E;YAC5E,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;QACnB,CAAC;IACH,CAAC;IAED,yEAAyE;IACzE,yEAAyE;IACzE,2EAA2E;IAC3E,MAAM,YAAY,GAAG,CAAC,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IACtD,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACnC,KAAK,MAAM,QAAQ,IAAI,YAAY,EAAE,CAAC;QACpC,IAAI,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,EAAE,CAAC;YACxB,MAAM,OAAO,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,QAAQ,IAAI,CAAC,CAAC,WAAW,EAAE,KAAK,QAAQ,CAAC,CAAC;YACrF,IAAI,OAAO,EAAE,CAAC;gBACZ,MAAM,CAAC,IAAI,CAAC;oBACV,KAAK,EAAE,OAAO;oBACd,MAAM,EAAE,aAAa;oBACrB,OAAO,EAAE,oBAAoB,OAAO,wBAAwB,QAAQ,kCAAkC;iBACvG,CAAC,CAAC;YACL,CAAC;QACH,CAAC;IACH,CAAC;IACD,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtB,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;IACvC,CAAC;IAED,MAAM,MAAM,GAAG,iBAAiB,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IAEjD,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC;QACpB,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YACxC,MAAM,CAAC,IAAI,CAAC;gBACV,KAAK,EAAE,OAAO;gBACd,MAAM,EAAE,aAAa;gBACrB,OAAO,EAAE,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,KAAK,CAAC,OAAO,EAAE;aACrD,CAAC,CAAC;QACL,CAAC;QACD,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;IACvC,CAAC;IAED,OAAO,EAAE,WAAW,EAAE,MAAM,CAAC,IAAmB,EAAE,MAAM,EAAE,CAAC;AAC7D,CAAC"}

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

@@ -106,6 +106,10 @@ function extractNormativeStatement(section) {
         if (line.match(/^#{1,6}\s+/)) {
             break;
         }
+        // Strip apply workflow marker comments (MODIFIED/ADDED markers)
+        if (line.match(/^<!--\s*(MODIFIED|ADDED)\s+by\s+change:/)) {
+            continue;
+        }
         normativeLines.push(line);
     }
     const text = normativeLines.join('\n').trim();

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

@@ -1 +1 @@
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package/dist/core/parser/task-parser.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"task-parser.d.ts","sourceRoot":"","sources":["../../../src/core/parser/task-parser.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,YAAY,CAAC;AAKtE;;GAEG;AACH,wBAAgB,UAAU,CACxB,QAAQ,EAAE,OAAO,EAAE,GAClB;IAAE,KAAK,EAAE,cAAc,EAAE,CAAC;IAAC,MAAM,EAAE,UAAU,EAAE,CAAA;CAAE,CAyBnD"}
+{"version":3,"file":"task-parser.d.ts","sourceRoot":"","sources":["../../../src/core/parser/task-parser.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,YAAY,CAAC;AAYtE;;GAEG;AACH,wBAAgB,UAAU,CACxB,QAAQ,EAAE,OAAO,EAAE,GAClB;IAAE,KAAK,EAAE,cAAc,EAAE,CAAC;IAAC,MAAM,EAAE,UAAU,EAAE,CAAA;CAAE,CAsCnD"}

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

@@ -1,5 +1,11 @@
 import { findSection } from './section-parser.js';
+// Full task line with content. Required by `parseTasks` to both capture
+// the completion state and record meaningful text.
 const TASK_REGEX = /^-\s+\[([ xX])\]\s+(.+)$/;
+// Empty task line (no description after the checkbox, e.g. `- [ ]` or
+// `- [x]    `). These get flagged as parse warnings so users know a
+// placeholder checkbox won't count toward progress.
+const EMPTY_TASK_REGEX = /^-\s+\[([ xX])\]\s*$/;
 /**
  * Parse task checklist items from a Change note's Tasks section.
  */
@@ -21,6 +27,19 @@ export function parseTasks(sections) {
                 done: match[1] !== ' ',
                 line: taskSection.line + i + 1,
             });
+            continue;
+        }
+        // Empty checkbox: surface as a parse warning so the change author
+        // sees it instead of a silent "0 tasks" count. The warning is
+        // non-blocking — continue.ts/apply.ts still treat the Change as
+        // having the parsed tasks, but the user knows to fill in the line.
+        if (EMPTY_TASK_REGEX.test(lines[i])) {
+            errors.push({
+                level: 'warning',
+                source: 'task',
+                message: `Empty checklist item "${lines[i].trim()}" (no task description). Add text after the checkbox or remove the line.`,
+                line: taskSection.line + i + 1,
+            });
         }
     }
     return { tasks, errors };

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

@@ -1 +1 @@
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+{"version":3,"file":"task-parser.js","sourceRoot":"","sources":["../../../src/core/parser/task-parser.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAElD,wEAAwE;AACxE,mDAAmD;AACnD,MAAM,UAAU,GAAG,0BAA0B,CAAC;AAE9C,sEAAsE;AACtE,oEAAoE;AACpE,oDAAoD;AACpD,MAAM,gBAAgB,GAAG,sBAAsB,CAAC;AAEhD;;GAEG;AACH,MAAM,UAAU,UAAU,CACxB,QAAmB;IAEnB,MAAM,KAAK,GAAqB,EAAE,CAAC;IACnC,MAAM,MAAM,GAAiB,EAAE,CAAC;IAEhC,MAAM,WAAW,GAAG,WAAW,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IACnD,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAC3B,CAAC;IAED,8FAA8F;IAC9F,mEAAmE;IACnE,MAAM,KAAK,GAAG,WAAW,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;IAE9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QACzC,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,CAAC,IAAI,CAAC;gBACT,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE;gBACrB,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG;gBACtB,IAAI,EAAE,WAAW,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC;aAC/B,CAAC,CAAC;YACH,SAAS;QACX,CAAC;QACD,kEAAkE;QAClE,8DAA8D;QAC9D,gEAAgE;QAChE,mEAAmE;QACnE,IAAI,gBAAgB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACpC,MAAM,CAAC,IAAI,CAAC;gBACV,KAAK,EAAE,SAAS;gBAChB,MAAM,EAAE,MAAM;gBACd,OAAO,EAAE,yBAAyB,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,0EAA0E;gBAC3H,IAAI,EAAE,WAAW,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC;aAC/B,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;AAC3B,CAAC;AAED,SAAS,gBAAgB,CAAC,OAAgB;IACxC,IAAI,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC;IAC9B,KAAK,MAAM,KAAK,IAAI,OAAO,CAAC,QAAQ,EAAE,CAAC;QACrC,OAAO,IAAI,IAAI,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAC;IAC5C,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/dist/core/parser/wikilink-parser.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"wikilink-parser.d.ts","sourceRoot":"","sources":["../../../src/core/parser/wikilink-parser.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,kBAAkB,EAAE,UAAU,EAAE,MAAM,YAAY,CAAC;AAKjE;;;GAGG;AACH,wBAAgB,gBAAgB,CAC9B,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,aAAa,GAAG,MAAM,EAChC,SAAS,GAAE,MAAU,GACpB;IAAE,SAAS,EAAE,kBAAkB,EAAE,CAAC;IAAC,MAAM,EAAE,UAAU,EAAE,CAAA;CAAE,CAuD3D;AAED;;;GAGG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAe5D;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,kBAAkB,EAAE,GAAG,MAAM,EAAE,CAM/E"}
+{"version":3,"file":"wikilink-parser.d.ts","sourceRoot":"","sources":["../../../src/core/parser/wikilink-parser.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,kBAAkB,EAAE,UAAU,EAAE,MAAM,YAAY,CAAC;AAKjE;;;GAGG;AACH,wBAAgB,gBAAgB,CAC9B,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,aAAa,GAAG,MAAM,EAChC,SAAS,GAAE,MAAU,GACpB;IAAE,SAAS,EAAE,kBAAkB,EAAE,CAAC;IAAC,MAAM,EAAE,UAAU,EAAE,CAAA;CAAE,CAwE3D;AAED;;;GAGG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAe5D;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,kBAAkB,EAAE,GAAG,MAAM,EAAE,CAM/E"}

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

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

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