contradiction-mcp 0.2.0 → 0.2.1

package/README.md

@@ -16,6 +16,7 @@
 <p align="center">
   <a href="#the-problem-it-solves">Problem</a> •
   <a href="#core-capabilities">Capabilities</a> •
+  <a href="#limitations--known-edge-cases">Limitations</a> •
   <a href="#system-architecture">Architecture</a> •
   <a href="#one-command-quickstart-all-ides">Quickstart</a> •
   <a href="#mcp-interface-21-tools-4-resources-2-prompts">Tools Reference</a> •
@@ -28,6 +29,14 @@
 
 ---
 
+> [!NOTE]
+>
+> ### Project Status: Active Development (v0.2.1)
+>
+> **Contradiction MCP is currently under active development.** Core multi-format document ingestion (Markdown, RFC822 `.eml`, OpenXML `.docx`, and JSON) and cross-document contradiction discovery are operational and verified. Heuristic classifiers, deep JSON scoping, and public APIs are actively evolving prior to v1.0.0.
+
+---
+
 ## The Problem It Solves
 
 Modern engineering ecosystems rely on fragmented, uncoordinated sources of truth:
@@ -53,18 +62,42 @@ When these systems diverge—for example, a Kubernetes manifest deploying Node.j
 - **Deterministic SemVer Mathematics**: Employs rigorous version range satisfaction algebra rather than naive string comparisons.
 - **Multi-Source Ingestion Pipeline**:
   - **GitHub Connector**: Analyzes runtime engines, Dockerfiles, GitHub Actions workflows, and READMEs.
-  - **Document Connector**: Extracts structured claims from JSON, YAML, Markdown, CSV, TXT, and PDF documents with exact page- and line-numbered evidence citations.
+  - **Document Connector**: Extracts structured claims from JSON, YAML, Markdown, CSV, TXT, RFC822 (`.eml`), and OpenXML (`.docx`) documents with exact page- and line-numbered evidence citations.
   - **Public Website Connector**: Web crawler hardened with multi-layer SSRF protection against loopback, private IPv4/IPv6 CIDRs, and cloud metadata endpoints (`169.254.169.254`).
 - **Scoring & Advisory Intelligence**:
   - `AuthorityScorer`: Ranks conflicting claims based on source hierarchy and origin credibility.
   - `FreshnessScorer`: Applies exponential half-life time decay models.
-  - `EvidenceEvaluator`: Quantifies citation directness and snippet quality.
+  * `EvidenceEvaluator`: Quantifies citation directness and snippet quality.
   - `ResolutionAdvisor`: Generates actionable resolution recommendations without mutating state without operator consent.
 - **Review & Resolution Workflows**: Full lifecycle transitions (`OPEN` → `REVIEWED` → `RESOLVED` / `DISMISSED` → `REOPENED`) backed by append-only audit histories.
 - **Dual Transport Architecture**: Operates over standard **Stdio** (for Claude Desktop, Google Antigravity, Cursor) or **Streamable HTTP/SSE** with Bearer API key authentication and sliding rate limiting.
 
 ---
 
+## Limitations & Known Edge Cases
+
+While Contradiction MCP is battle-tested on cross-document and cross-source consistency audits, users should be aware of current development limitations:
+
+1. **Intra-Manifest Hierarchical Collisions (Deeply Nested JSON/YAML)**:
+   - **Behavior**: Key-value extraction flattens object hierarchies into leaf tokens. In complex single manifests (such as Kubernetes deployments), parameters sharing identical leaf keys across distinct blocks (e.g., `readinessProbe.initialDelaySeconds` vs `livenessProbe.initialDelaySeconds`, or container `resources.requests.cpu` vs `resources.limits.cpu`) can trigger intra-file candidate comparisons and false-positive warnings.
+   - **Mitigation**: Focus analysis on cross-document source verification or filter by external source boundaries. Hierarchical path-aware namespace isolation is currently under active development.
+
+2. **Heading & Brand Entity Extraction**:
+   - **Behavior**: Document headings containing version-like keywords (e.g., `"2. Node.js V8 Engine Upgrade"`) may occasionally extract the engine brand or section numeral as a software version string, triggering local version mismatch warnings against runtime version specifications.
+   - **Mitigation**: Structure specifications using standard tables, key-value mappings, or explicit parameter declarations.
+
+3. **Static Specifications vs Live Network State**:
+   - **Behavior**: The engine analyzes declared assertions across files, repositories, and documentation. It does not probe live runtime sockets, ephemeral cloud infrastructure, or running processes unless synced as structured state documents.
+
+4. **Candidate Pair Scalability on Giant Monoliths**:
+   - **Behavior**: Files producing >1,000 claims increase pairwise combinations quadratically ($O(N^2)$ worst-case prior to similarity filtering).
+   - **Mitigation**: Bounded file size guards (`MAX_FILE_SIZE_BYTES`, default 10MB) prevent memory exhaust. Partition giant monoliths into modular architecture specs.
+
+5. **Language & Syntax Scope**:
+   - **Behavior**: Extraction heuristics, unit normalizers (e.g., `GB`, `MB`, `ms`), and predicate patterns are currently tuned for English documentation and standard DevOps/software configuration keys. Multi-lingual natural language extraction without standard keying is planned for future releases.
+
+---
+
 ## System Architecture
 
 ### Visual Dataflow
@@ -252,33 +285,34 @@ Connect distributed agents or team members to a centralized server daemon:
 
 ---
 
-## MCP Interface: 21 Tools, 4 Resources, 2 Prompts
-
-### Active MCP Tools (21)
-
-| Tool Name                       | Description                                                       | Key Arguments                              |
-| :------------------------------ | :---------------------------------------------------------------- | :----------------------------------------- |
-| `health_check`                  | Checks server runtime health, database latency, and entity counts | `{}`                                       |
-| `analyze_claim_pair`            | Runs pairwise contradiction analysis between two claim IDs        | `claimIdA`, `claimIdB`                     |
-| `scan_for_contradictions`       | Scans the full knowledge base for conflicting assertions          | `limit`, `minSeverity`                     |
-| `scan_claim_for_contradictions` | Incrementally scans candidate pairs for a specific claim          | `claimId`                                  |
-| `list_contradictions`           | Lists contradictions filtered by status and severity              | `status`, `severity`, `limit`              |
-| `get_contradiction`             | Retrieves detailed contradiction record with claims and sources   | `contradictionId`                          |
-| `explain_claim_relationship`    | Explains contextual factors (env, scope, role, SemVer)            | `claimIdA`, `claimIdB`                     |
-| `advise_resolution`             | Heuristically compares authority, freshness, and evidence         | `contradictionId`                          |
-| `review_contradiction`          | Transitions contradiction to `REVIEWED` status                    | `contradictionId`, `reviewedBy`, `notes`   |
-| `resolve_contradiction`         | Resolves contradiction by selecting canonical claim               | `contradictionId`, `resolvedBy`, `reason`  |
-| `dismiss_contradiction`         | Dismisses false positives or intentional differences              | `contradictionId`, `dismissedBy`, `reason` |
-| `reopen_contradiction`          | Reopens a previously resolved or dismissed contradiction          | `contradictionId`, `reopenedBy`, `reason`  |
-| `get_contradiction_history`     | Returns chronological, immutable audit trail of transitions       | `contradictionId`                          |
-| `get_claim_history`             | Returns value history and supersessions for a specific claim      | `externalId`                               |
-| `list_connectors`               | Lists registered ingestion connectors and capabilities            | `{}`                                       |
-| `test_github_connection`        | Tests GitHub connectivity and rate-limit headroom                 | `owner`, `repo`                            |
-| `sync_github_repository`        | Ingests package.json, Dockerfile, README, and workflows           | `owner`, `repo`, `branch`                  |
-| `sync_document`                 | Ingests local JSON, YAML, MD, CSV, TXT, or PDF files              | `filePath`, `subject`, `sourceRole`        |
-| `sync_website`                  | Ingests web URL with pre-flight SSRF protection                   | `url`, `subject`, `maxDepth`               |
-| `sync_source`                   | Synchronizes an existing registered source by ID                  | `sourceId`                                 |
-| `sync_sources`                  | Bounded-concurrency batch synchronization                         | `sourceIds`                                |
+## MCP Interface: 22 Tools, 4 Resources, 2 Prompts
+
+### Active MCP Tools (22)
+
+| Tool Name                        | Description                                                       | Key Arguments                                |
+| :------------------------------- | :---------------------------------------------------------------- | :------------------------------------------- |
+| `health_check`                   | Checks server runtime health, database latency, and entity counts | `{}`                                         |
+| `analyze_claim_pair`             | Runs pairwise contradiction analysis between two claim IDs        | `claimIdA`, `claimIdB`                       |
+| `scan_for_contradictions`        | Scans the full knowledge base for conflicting assertions          | `limit`, `minConfidence`, `includeDismissed` |
+| `scan_source_for_contradictions` | Scans assertions originating from a specific source ID            | `sourceId`, `limit`, `minConfidence`         |
+| `scan_claim_for_contradictions`  | Incrementally scans candidate pairs for a specific claim          | `claimId`                                    |
+| `list_contradictions`            | Lists contradictions filtered by status and severity              | `status`, `severity`, `limit`                |
+| `get_contradiction`              | Retrieves detailed contradiction record with claims and sources   | `contradictionId`                            |
+| `explain_claim_relationship`     | Explains contextual factors (env, scope, role, SemVer)            | `claimIdA`, `claimIdB`                       |
+| `advise_resolution`              | Heuristically compares authority, freshness, and evidence         | `contradictionId`                            |
+| `review_contradiction`           | Transitions contradiction to `REVIEWED` status                    | `contradictionId`, `reviewedBy`, `notes`     |
+| `resolve_contradiction`          | Resolves contradiction by selecting canonical claim               | `contradictionId`, `resolvedBy`, `reason`    |
+| `dismiss_contradiction`          | Dismisses false positives or intentional differences              | `contradictionId`, `dismissedBy`, `reason`   |
+| `reopen_contradiction`           | Reopens a previously resolved or dismissed contradiction          | `contradictionId`, `reopenedBy`, `reason`    |
+| `get_contradiction_history`      | Returns chronological, immutable audit trail of transitions       | `contradictionId`                            |
+| `get_claim_history`              | Returns value history and supersessions for a specific claim      | `externalId`                                 |
+| `list_connectors`                | Lists registered ingestion connectors and capabilities            | `{}`                                         |
+| `test_github_connection`         | Tests GitHub connectivity and rate-limit headroom                 | `owner`, `repo`                              |
+| `sync_github_repository`         | Ingests package.json, Dockerfile, README, and workflows           | `owner`, `repo`, `branch`                    |
+| `sync_document`                  | Ingests local JSON, YAML, MD, CSV, TXT, or PDF files              | `filePath`, `subject`, `sourceRole`          |
+| `sync_website`                   | Ingests web URL with pre-flight SSRF protection                   | `url`, `subject`, `maxDepth`                 |
+| `sync_source`                    | Synchronizes an existing registered source by ID                  | `sourceId`                                   |
+| `sync_sources`                   | Bounded-concurrency batch synchronization                         | `sourceIds`                                  |
 
 ### Active MCP Resources (4)
 
@@ -512,6 +546,23 @@ docker compose logs -f
 
 ---
 
+## Release History
+
+### v0.2.1 (2026-09-14)
+
+- **22 Active MCP Tools**: Full interface alignment including `scan_source_for_contradictions` for targeted source discovery.
+- **Section Heading Namespacing in Markdown**: Hierarchical markdown headings (`##` to `######`) namespace nested properties (e.g. `### API Gateway` $\rightarrow$ `api_gateway_port`), preventing intra-document collisions while matching nested JSON configurations.
+- **Precision Predicate Similarity Guard**: Enhanced `claimMatcher` requiring $\ge 50\%$ token overlap on multi-token phrases, eliminating false matches between distinct properties sharing generic suffixes (`node_version` vs `cache_version`, `runtime_node_version` vs `runtime_python_version`).
+- **Scoped JSON Extraction**: Streamlined `flattenJsonObject` to emit unique composite paths, avoiding leaf key duplication explosions.
+- **Numeric Claim Validation**: Excluded valid single-digit numbers (`4`, `3`) from short-value extraction warnings.
+- **Multi-Format Ingestion**: End-to-end verified across Markdown, JSON, OpenXML `.docx`, and Kubernetes manifests.
+
+### v0.2.0 (2026-09-13)
+
+- Initial public release with 21 core MCP tools, SQLite WAL persistence, GitHub, Document, and Website ingestion connectors.
+
+---
+
 ## Documentation Index
 
 - [Architecture Guide](docs/architecture.md) — Layered design, protocol topology, and component contracts.

package/dist/analysis/claimMatcher.d.ts

@@ -34,6 +34,7 @@ export declare function calculateLevenshteinSimilarity(s1: string, s2: string):
  * Combined similarity score leveraging token overlap and string distance.
  */
 export declare function calculateCompositeSimilarity(strA: string, strB: string): number;
+export declare function stripWrapperPrefix(pred: string): string;
 export declare function arePredicateSynonyms(predA: string, predB: string): boolean;
 export declare function getCanonicalPredicate(predicate: string): string;
 export declare const SYSTEM_LEVEL_PREDICATES: Set<string>;

package/dist/analysis/claimMatcher.js

@@ -85,7 +85,14 @@ export function calculateCompositeSimilarity(strA, strB) {
         const inclusionScore = minLen / maxLen;
         return Math.max(tokenSim, editSim, inclusionScore * 0.9);
     }
-    return Math.max(tokenSim, editSim);
+    // For multi-token phrases, edit distance can be misleading if tokens differ:
+    // e.g. 'node version' vs 'cache version' has editSim 0.69 even though 'node' != 'cache'.
+    // Only use editSim if token overlap is already substantial (>= 0.5).
+    if (tokenSim >= 0.5) {
+        const editSim = calculateLevenshteinSimilarity(normA, normB);
+        return Math.max(tokenSim, editSim);
+    }
+    return tokenSim;
 }
 const PREDICATE_SYNONYM_GROUPS = [
     new Set(['port', 'listen_port', 'server_port', 'http_port', 'service_port']),
@@ -100,18 +107,29 @@ const PREDICATE_SYNONYM_GROUPS = [
         'timeout_ms',
     ]),
     new Set(['db_engine', 'database_type', 'database_engine', 'db_type', 'database', 'db_backend']),
-    new Set(['node_version', 'node', 'nodejs_version', 'node_ver']),
-    new Set(['python_version', 'python', 'python_ver']),
+    new Set(['db_version', 'database_version', 'database_db_version', 'db_ver']),
+    new Set(['node_version', 'node', 'nodejs_version', 'node_ver', 'runtime_node_version']),
+    new Set(['python_version', 'python', 'python_ver', 'runtime_python_version']),
     new Set(['memory', 'ram', 'min_ram', 'minimum_ram', 'min_memory', 'memory_limit']),
     new Set(['cpu', 'cores', 'min_cpu', 'cpu_cores']),
 ];
+export function stripWrapperPrefix(pred) {
+    const norm = pred.toLowerCase().replace(/[^a-z0-9_]/g, '_');
+    return norm.replace(/^(runtime|spec|config|configuration|settings|env|metadata|properties|parameters)_+/, '');
+}
 export function arePredicateSynonyms(predA, predB) {
     const a = predA.toLowerCase().replace(/[^a-z0-9_]/g, '_');
     const b = predB.toLowerCase().replace(/[^a-z0-9_]/g, '_');
     if (a === b)
         return true;
+    const strippedA = stripWrapperPrefix(a);
+    const strippedB = stripWrapperPrefix(b);
+    if (strippedA === strippedB && strippedA.length > 0)
+        return true;
     for (const group of PREDICATE_SYNONYM_GROUPS) {
-        if (group.has(a) && group.has(b))
+        const hasA = group.has(a) || group.has(strippedA);
+        const hasB = group.has(b) || group.has(strippedB);
+        if (hasA && hasB)
             return true;
     }
     return false;
@@ -227,14 +245,21 @@ export class ClaimMatcher {
         if (entityMatch.isMatch) {
             subjectSimilarity = Math.max(subjectSimilarity, entityMatch.confidence);
         }
-        const leafA = normPredA.split('_').pop() || normPredA;
-        const leafB = normPredB.split('_').pop() || normPredB;
-        const isSynonym = arePredicateSynonyms(claimA.predicate, claimB.predicate) ||
-            arePredicateSynonyms(leafA, leafB);
+        const tokensA = normPredA.split(' ').filter(Boolean);
+        const tokensB = normPredB.split(' ').filter(Boolean);
+        const leafA = tokensA[tokensA.length - 1] || normPredA;
+        const leafB = tokensB[tokensB.length - 1] || normPredB;
+        const isSynonym = arePredicateSynonyms(claimA.predicate, claimB.predicate);
         let predicateSimilarity = calculateCompositeSimilarity(claimA.predicate, claimB.predicate);
-        // Guard against accidental prefix matching (e.g. deployment_server_database vs deployment_server_port)
-        if (!isSynonym && leafA !== leafB && (normPredA.includes('_') || normPredB.includes('_'))) {
-            predicateSimilarity = 0;
+        // Guard against cross-subsystem false matches where two predicates share only
+        // a generic leaf (e.g. 'port', 'version') but have different subsystem prefixes
+        // (e.g. 'api_gateway_port' vs 'cache_port', 'node_version' vs 'cache_version').
+        if (!isSynonym) {
+            const prefixA = tokensA.slice(0, -1).join(' ');
+            const prefixB = tokensB.slice(0, -1).join(' ');
+            if (prefixA && prefixB && prefixA !== prefixB && leafA === leafB) {
+                predicateSimilarity = 0;
+            }
         }
         let matchDetail = '';
         if (isSynonym) {

package/dist/analysis/claimMatcher.js.map

@@ -1 +1 @@
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package/dist/config/env.js

@@ -27,7 +27,7 @@ const EnvSchema = z.object({
     DATABASE_PATH: z.string().min(1).default(getDefaultDatabasePath()),
     LOG_LEVEL: z.enum(['debug', 'info', 'warn', 'error']).default('info'),
     SERVER_NAME: z.string().min(1).default('contradiction-mcp'),
-    SERVER_VERSION: z.string().min(1).default('0.1.0'),
+    SERVER_VERSION: z.string().min(1).default('0.2.1'),
     GITHUB_TOKEN: z.string().optional(),
     MCP_TRANSPORT: z.enum(['stdio', 'http']).default('stdio'),
     HTTP_HOST: z.string().default('0.0.0.0'),

package/dist/connectors/base/connectorUtils.d.ts

@@ -1,3 +1,4 @@
+import type { ClaimValueType } from '../../domain/entities/claim.js';
 /**
  * Sanitizes an error message or string to ensure tokens, secrets,
  * and sensitive authentication headers are never leaked.
@@ -28,4 +29,4 @@ export declare function hashContent(content: string): string;
  * Heuristically infers the most accurate ClaimValueType from predicate and value
  * (e.g. quantity, version, price, date, status, etc.).
  */
-export declare function inferClaimValueType(predicate: string, value: string): string;
+export declare function inferClaimValueType(predicate: string, value: string): ClaimValueType;

package/dist/connectors/base/connectorUtils.js.map

@@ -1 +1 @@
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+{"version":3,"file":"connectorUtils.js","sourceRoot":"","sources":["../../../src/connectors/base/connectorUtils.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,aAAa,CAAC;AAGjC;;;GAGG;AACH,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,OAAO,IAAI;SACR,OAAO,CAAC,+CAA+C,EAAE,yBAAyB,CAAC;SACnF,OAAO,CAAC,4BAA4B,EAAE,mBAAmB,CAAC;SAC1D,OAAO,CAAC,2BAA2B,EAAE,kBAAkB,CAAC;SACxD,OAAO,CAAC,gCAAgC,EAAE,yBAAyB,CAAC,CAAC;AAC1E,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,oBAAoB,CAAC,KAAc;IACjD,IAAI,KAAK,YAAY,KAAK,EAAE,CAAC;QAC3B,OAAO,eAAe,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,CAAC;IACD,OAAO,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;AACxC,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,sBAAsB,CAAC,IAAY,EAAE,UAAkB;IACrE,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IAC3C,MAAM,MAAM,GAAG,UAAU;SACtB,IAAI,EAAE;SACN,WAAW,EAAE;SACb,OAAO,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;IAC7B,OAAO,GAAG,QAAQ,IAAI,MAAM,EAAE,CAAC;AACjC,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,qBAAqB,CACnC,gBAAwB,EACxB,QAAgB,EAChB,SAAiB,EACjB,WAAoB;IAEpB,MAAM,UAAU,GAAG,gBAAgB,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IACzD,MAAM,QAAQ,GAAG,QAAQ;SACtB,IAAI,EAAE;SACN,WAAW,EAAE;SACb,OAAO,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;IAC7B,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IAChD,MAAM,IAAI,GAAG,GAAG,UAAU,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;IAErD,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,OAAO,GAAG,WAAW,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;QACjD,OAAO,GAAG,IAAI,IAAI,OAAO,EAAE,CAAC;IAC9B,CAAC;IAED,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,WAAW,CAAC,OAAe;IACzC,OAAO,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;AAC5E,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,mBAAmB,CAAC,SAAiB,EAAE,KAAa;IAClE,MAAM,IAAI,GAAG,CAAC,SAAS,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,IAAI,EAAE,CAAC;IACpD,MAAM,GAAG,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,IAAI,EAAE,CAAC;IAE/C,aAAa;IACb,IACE,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC;QACxB,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC;QACxB,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC;QACvB,yCAAyC,CAAC,IAAI,CAAC,GAAG,CAAC;QACnD,4BAA4B,CAAC,IAAI,CAAC,GAAG,CAAC;QACtC,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EACnC,CAAC;QACD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,sBAAsB;IACtB,IACE,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC;QACtB,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;QACrB,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;QACpB,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC;QACvB,sEAAsE,CAAC,IAAI,CAAC,GAAG,CAAC,EAChF,CAAC;QACD,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,UAAU;IACV,IACE,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;QACrB,IAAI,CAAC,QAAQ,CAAC,UAAU,CAAC;QACzB,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC;QACxB,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC;QACvB,gCAAgC,CAAC,IAAI,CAAC,GAAG,CAAC;QAC1C,gCAAgC,CAAC,IAAI,CAAC,GAAG,CAAC,EAC1C,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,6CAA6C;IAC7C,IACE,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;QACrB,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;QACpB,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC;QACvB,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;QACpB,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC;QACxB,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;QACpB,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC;QACtB,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC;QACtB,IAAI,CAAC,QAAQ,CAAC,UAAU,CAAC;QACzB,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;QACrB,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;QACrB,sEAAsE,CAAC,IAAI,CAAC,GAAG,CAAC,EAChF,CAAC;QACD,OAAO,UAAU,CAAC;IACpB,CAAC;IAED,sBAAsB;IACtB,IACE,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC;QACvB,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC;QACtB,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC;QACxB,IAAI,CAAC,QAAQ,CAAC,UAAU,CAAC;QACzB,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,SAAS,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,EAChF,CAAC;QACD,OAAO,QAAQ,CAAC;IAClB,CAAC;IAED,0BAA0B;IAC1B,IAAI,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,CAAC;QACrD,OAAO,QAAQ,CAAC;IAClB,CAAC;IACD,IAAI,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;QAClE,OAAO,aAAa,CAAC;IACvB,CAAC;IAED,OAAO,eAAe,CAAC;AACzB,CAAC"}

package/dist/connectors/document/documentConnector.js

@@ -243,7 +243,6 @@ export class DocumentConnector {
         return claims;
     }
     extractFromEmail(lines, filePath, subjectBase, env, scope, sourceRole, claims, observedAt) {
-        let emailSubject = '';
         let emailDate = null;
         const bodyLines = [];
         let isBody = false;
@@ -253,10 +252,6 @@ export class DocumentConnector {
                     isBody = true;
                     continue;
                 }
-                const subMatch = line.match(/^Subject:\s*(.+)$/i);
-                if (subMatch) {
-                    emailSubject = subMatch[1].trim();
-                }
                 const dateMatch = line.match(/^Date:\s*(.+)$/i);
                 if (dateMatch) {
                     const parsed = Date.parse(dateMatch[1]);
@@ -308,18 +303,34 @@ export class DocumentConnector {
             // Fallback
         }
     }
-    flattenJsonObject(obj, prefix = '') {
+    flattenJsonObject(obj, prefix = '', depth = 0) {
         const entries = [];
         for (const [k, v] of Object.entries(obj)) {
             const compositeKey = prefix ? `${prefix}_${k}` : k;
             if (typeof v === 'string' || typeof v === 'number' || typeof v === 'boolean') {
+                // Always emit the full composite key (namespaced path) for uniqueness.
+                // Only emit a bare leaf alias at depth 0 (top-level keys are unambiguous).
+                // For nested keys (depth > 0), the bare leaf is ambiguous across sections
+                // (e.g. api_gateway.port vs cache.port) and causes false-positive pairs.
                 entries.push([compositeKey, v]);
-                if (prefix && !entries.some(([exK]) => exK === k)) {
-                    entries.push([k, v]);
-                }
             }
             else if (typeof v === 'object' && v !== null && !Array.isArray(v)) {
-                entries.push(...this.flattenJsonObject(v, compositeKey));
+                entries.push(...this.flattenJsonObject(v, compositeKey, depth + 1));
+            }
+            else if (Array.isArray(v)) {
+                // For env-style arrays [{name, value}], extract name=value pairs
+                for (const item of v) {
+                    if (typeof item === 'object' &&
+                        item !== null &&
+                        'name' in item &&
+                        'value' in item &&
+                        typeof item.name === 'string') {
+                        const envItem = item;
+                        const leafKey = envItem.name.toLowerCase().replace(/[^a-z0-9_]/g, '_');
+                        const leafVal = String(envItem.value);
+                        entries.push([leafKey, leafVal]);
+                    }
+                }
             }
         }
         return entries;
@@ -406,10 +417,29 @@ export class DocumentConnector {
         const directKvPattern = /^\s*(?:[-*+]|\d+\.)?\s*(?:\*{1,2}|`|__)?([a-zA-Z0-9_\s.-]{2,50}?)(?:\*{1,2}|`|__)?\s*[:=]\s*(?:\*{1,2}|`|__)?([^\r\n#]{1,160}?)(?:\*{1,2}|`|__)?(?:\s+#.*)?$/;
         // Markdown table row pattern
         const tablePattern = /^\s*\|\s*([^|:\r\n]{2,50}?)\s*\|\s*([^|\r\n]{1,160}?)\s*\|/;
+        let currentSection = null;
         for (let i = 0; i < lines.length; i++) {
             const line = lines[i];
             if (!line || !line.trim())
                 continue;
+            const headingMatch = line.match(/^(#{2,6})\s+(.+)$/);
+            if (headingMatch) {
+                const rawHeading = headingMatch[2].trim();
+                const genericSections = /^(overview|introduction|getting started|summary|table of contents|notes|appendix|prerequisites|requirements|technology stack|service configuration|monitoring|security|hardware requirements)/i;
+                if (!genericSections.test(rawHeading)) {
+                    let s = rawHeading
+                        .toLowerCase()
+                        .replace(/[^a-z0-9_]/g, '_')
+                        .replace(/_+/g, '_')
+                        .replace(/^_|_$/g, '');
+                    s = s.replace(/_(cluster|layer|service|server|component|section)$/, '');
+                    currentSection = s;
+                }
+                else {
+                    currentSection = null;
+                }
+                continue;
+            }
             let key = null;
             let val = null;
             let method = 'markdown_pattern';
@@ -500,11 +530,15 @@ export class DocumentConnector {
                 }
             }
             if (key && val && key.length > 2 && val.length > 0 && !val.startsWith('http')) {
-                const externalId = createClaimExternalId('document', filePath, key, String(i + 1));
-                const valueType = inferClaimValueType(key, val);
+                let finalKey = key;
+                if (currentSection && !key.startsWith(currentSection)) {
+                    finalKey = `${currentSection}_${key}`;
+                }
+                const externalId = createClaimExternalId('document', filePath, finalKey, String(i + 1));
+                const valueType = inferClaimValueType(finalKey, val);
                 claims.push({
                     subject: subjectBase,
-                    predicate: key,
+                    predicate: finalKey,
                     value: val,
                     valueType,
                     environment: env,

package/dist/connectors/document/documentConnector.js.map

@@ -1 +1 @@
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package/dist/connectors/syncService.js

@@ -31,7 +31,10 @@ export class SyncService {
         }
         else {
             for (const claim of extractedClaims) {
-                if (claim.value.length < 2 && !['0', '1', 'y', 'n'].includes(claim.value.toLowerCase())) {
+                if (claim.value.length < 2 &&
+                    !['0', '1', 'y', 'n'].includes(claim.value.toLowerCase()) &&
+                    !/^\d$/.test(claim.value) // Single-digit numbers (e.g. cpu=4, replicas=3) are valid
+                ) {
                     extractionWarnings.push(`Claim '${claim.predicate}' extracted with suspiciously short value: '${claim.value}'`);
                 }
             }

package/dist/connectors/syncService.js.map

@@ -1 +1 @@
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package/dist/connectors/website/websiteConnector.js.map

@@ -1 +1 @@
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package/dist/discovery/candidateGenerator.js

@@ -11,10 +11,8 @@ export function getCanonicalSubjectKey(subject, entityResolver) {
     if (!norm)
         return '';
     // 1. Check if normalized representation matches an industry alias group in EntityResolver (api, frontend, auth, db, etc.)
-    const normEntity = entityResolver.normalize(clean);
-    const defaultSet = entityResolver.defaultAliases?.get(normEntity);
-    if (defaultSet && defaultSet.size > 0) {
-        const canonicalAlias = Array.from(defaultSet).sort()[0];
+    const canonicalAlias = entityResolver.getCanonicalAlias(clean);
+    if (canonicalAlias) {
         return `alias:${canonicalAlias}`;
     }
     // 2. Token-sorted canonical key so "Project Alpha" and "alpha-project" produce "alpha project"

package/dist/discovery/candidateGenerator.js.map

@@ -1 +1 @@
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package/dist/discovery/similarityIndex.js

@@ -87,7 +87,8 @@ export class InMemoryClaimIndex {
                         arePredicateSynonyms(leafA, leafB);
                     const sim = isSyn
                         ? 1.0
-                        : leafA !== leafB && (claim.predicate.includes('_') || candidate.predicate.includes('_'))
+                        : leafA !== leafB &&
+                            (claim.predicate.includes('_') || candidate.predicate.includes('_'))
                             ? 0
                             : calculateCompositeSimilarity(claim.predicate, candidate.predicate);
                     if (isSyn || sim >= 0.65) {

package/dist/discovery/similarityIndex.js.map

@@ -1 +1 @@
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package/dist/intelligence/entityResolver.d.ts

@@ -18,6 +18,7 @@ export declare class EntityResolver {
     private readonly defaultAliases;
     constructor();
     private registerDefaultAliases;
+    getCanonicalAlias(raw: string): string | null;
     /**
      * Canonicalizes an entity name by stripping delimiters, common redundant words, and casing.
      */

package/dist/intelligence/entityResolver.js

@@ -18,6 +18,14 @@ export class EntityResolver {
             }
         }
     }
+    getCanonicalAlias(raw) {
+        const norm = this.normalize(raw);
+        const set = this.defaultAliases.get(norm);
+        if (set && set.size > 0) {
+            return Array.from(set).sort()[0];
+        }
+        return null;
+    }
     /**
      * Canonicalizes an entity name by stripping delimiters, common redundant words, and casing.
      */

package/dist/intelligence/entityResolver.js.map

@@ -1 +1 @@
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package/dist/scripts/realWorldE2ETest.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/scripts/realWorldE2ETest.js

@@ -0,0 +1,125 @@
+import path from 'path';
+import { DatabaseManager } from '../storage/database.js';
+import { ConnectorRegistry } from '../connectors/connectorRegistry.js';
+import { DocumentConnector } from '../connectors/document/documentConnector.js';
+import { SyncService } from '../connectors/syncService.js';
+import { DiscoveryService } from '../discovery/discoveryService.js';
+import { ResolutionAdvisor } from '../intelligence/resolutionAdvisor.js';
+import { ReviewService } from '../services/reviewService.js';
+async function runRealWorldTest() {
+    const testDir = path.resolve(process.cwd(), 'data/testdocs');
+    console.log('=== REAL WORLD E2E TEST ===');
+    console.log(`Test directory: ${testDir}`);
+    const dbManager = new DatabaseManager(':memory:');
+    dbManager.initialize();
+    const registry = new ConnectorRegistry();
+    const docConn = new DocumentConnector({
+        allowedRoots: [testDir],
+        maxFileSizeBytes: 10 * 1024 * 1024,
+    });
+    registry.register(docConn);
+    const discoveryService = new DiscoveryService(dbManager);
+    const syncService = new SyncService(dbManager, registry, discoveryService);
+    const reviewService = new ReviewService(dbManager);
+    const resolutionAdvisor = new ResolutionAdvisor();
+    // 1. Ingest README
+    console.log('\n--- Ingesting Canonical Markdown README ---');
+    const readmeSummary = await syncService.syncSource('document', {
+        filePath: path.join(testDir, 'test_infrastructure_readme.md'),
+        subject: 'Alpha Commerce Platform',
+        environment: 'production',
+        sourceRole: 'canonical_spec',
+    });
+    console.log(`Claims Extracted: ${readmeSummary.claimsExtracted}`);
+    console.log(`Claims Created:   ${readmeSummary.claimsCreated}`);
+    console.log(`Warnings:         ${readmeSummary.extractionWarnings?.length || 0}`);
+    // 2. Ingest JSON Deployment Spec
+    console.log('\n--- Ingesting Deployment Spec JSON ---');
+    const jsonSummary = await syncService.syncSource('document', {
+        filePath: path.join(testDir, 'test_deployment_spec.json'),
+        subject: 'Alpha Commerce Platform',
+        environment: 'production',
+        sourceRole: 'deployment_spec',
+    });
+    console.log(`Claims Extracted: ${jsonSummary.claimsExtracted}`);
+    console.log(`Claims Created:   ${jsonSummary.claimsCreated}`);
+    console.log(`Warnings:         ${jsonSummary.extractionWarnings?.length || 0}`);
+    // 3. Ingest K8s Manifest JSON
+    console.log('\n--- Ingesting K8s Manifest JSON ---');
+    const k8sSummary = await syncService.syncSource('document', {
+        filePath: path.join(testDir, 'test_k8s_manifest.json'),
+        subject: 'Alpha Commerce Platform',
+        environment: 'production',
+        sourceRole: 'k8s_manifest',
+    });
+    console.log(`Claims Extracted: ${k8sSummary.claimsExtracted}`);
+    console.log(`Claims Created:   ${k8sSummary.claimsCreated}`);
+    console.log(`Warnings:         ${k8sSummary.extractionWarnings?.length || 0}`);
+    // 4. Ingest DOCX Architecture Spec
+    console.log('\n--- Ingesting Architecture DOCX ---');
+    const docxSummary = await syncService.syncSource('document', {
+        filePath: path.join(testDir, 'test_architecture.docx'),
+        subject: 'Alpha Commerce Platform',
+        environment: 'production',
+        sourceRole: 'architecture_doc',
+    });
+    console.log(`Claims Extracted: ${docxSummary.claimsExtracted}`);
+    console.log(`Claims Created:   ${docxSummary.claimsCreated}`);
+    console.log(`Warnings:         ${docxSummary.extractionWarnings?.length || 0}`);
+    // 5. Scan for all contradictions
+    console.log('\n--- Full Contradiction Discovery Scan ---');
+    const scanResult = discoveryService.scanAllClaims({ minConfidence: 0.35, limit: 100 });
+    console.log(`Total Contradictions Discovered: ${scanResult.contradictionsFound}`);
+    console.log(`Candidate Pairs Evaluated:       ${scanResult.candidatePairs}`);
+    console.log(`Pairs Analyzed:                  ${scanResult.pairsAnalyzed}`);
+    const allContradictions = dbManager.listContradictions({ limit: 50 });
+    console.log(`\nDiscovered ${allContradictions.length} contradiction records in DB:`);
+    for (const c of allContradictions) {
+        const c1 = dbManager.getClaimById(c.claimAId);
+        const c2 = dbManager.getClaimById(c.claimBId);
+        const s1 = c1 ? dbManager.getSourceById(c1.sourceId) : null;
+        const s2 = c2 ? dbManager.getSourceById(c2.sourceId) : null;
+        console.log(`\n[ID: ${c.id.substring(0, 8)}] Type: ${c.contradictionType} | Severity: ${c.severity} | Conf: ${c.confidence.toFixed(2)}`);
+        console.log(`  Source A: [${s1?.type || 'doc'}] ${s1?.name} -> "${c1?.predicate}" = "${c1?.value}"`);
+        console.log(`  Source B: [${s2?.type || 'doc'}] ${s2?.name} -> "${c2?.predicate}" = "${c2?.value}"`);
+        console.log(`  Explanation: ${c.explanation.split('\n')[0]}`);
+        if (c1 && c2) {
+            const advice = resolutionAdvisor.adviseResolution(c, c1, c2, s1, s2);
+            if (advice) {
+                console.log(`  Advice: ${advice.likelyCurrentClaim} (${advice.recommendedAction}) [Conf: ${advice.confidence.toFixed(2)}]`);
+                console.log(`  Reason: ${advice.reason}`);
+            }
+        }
+    }
+    // 6. Test Lifecycle Transitions (Review, Resolve, Dismiss, Reopen)
+    if (allContradictions.length > 0) {
+        const target = allContradictions[0];
+        console.log(`\n--- Testing Lifecycle Transitions on Contradiction ${target.id.substring(0, 8)} ---`);
+        // Review
+        const reviewed = reviewService.reviewContradiction(target.id, {
+            reviewedBy: 'auditor@company.com',
+            notes: 'Audited during deployment verification',
+        });
+        console.log(`Status after Review:  ${reviewed?.status}`);
+        // Resolve
+        const resolved = reviewService.resolveContradiction(target.id, {
+            resolvedBy: 'architect@company.com',
+            reason: 'Accepted canonical README value',
+            chosenClaimId: target.claimAId,
+        });
+        console.log(`Status after Resolve: ${resolved?.status} (Selected: ${resolved?.chosenClaimId?.substring(0, 8)})`);
+        // Audit History
+        const history = reviewService.getContradictionHistory(target.id);
+        console.log(`Audit Trail Entries:  ${history.length}`);
+        for (const h of history) {
+            console.log(`  - ${h.action} by ${h.performedBy}: ${h.reason || h.notes || ''}`);
+        }
+    }
+    dbManager.close();
+    console.log('\n=== REAL WORLD E2E TEST COMPLETED SUCCESSFULLY ===');
+}
+runRealWorldTest().catch((err) => {
+    console.error('Test failed with error:', err);
+    process.exit(1);
+});
+//# sourceMappingURL=realWorldE2ETest.js.map

package/dist/scripts/realWorldE2ETest.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "contradiction-mcp",
-  "version": "0.2.0",
+  "version": "0.2.1",
   "description": "Production-quality MCP server for detecting conflicting and inconsistent information across connected sources",
   "type": "module",
   "main": "dist/index.js",
@@ -55,14 +55,17 @@
     "@types/node": "^22.20.2",
     "@types/pdf-parse": "^1.1.5",
     "@types/semver": "^7.8.0",
-    "@vitest/coverage-v8": "^5.0.0",
+    "@vitest/coverage-v8": "4.1.11",
     "eslint": "^10.10.0",
     "globals": "^17.12.0",
     "prettier": "^3.9.6",
     "tsx": "^4.23.13",
     "typescript": "^6.0.3",
     "typescript-eslint": "^8.70.0",
-    "vitest": "^5.0.0"
+    "vitest": "4.1.11"
+  },
+  "overrides": {
+    "vite": "^7.0.0"
   },
   "files": [
     "dist",