feat: add neural extraction APIs with NounType taxonomy

Add brain.extract() and brain.extractConcepts() methods that use
NeuralEntityExtractor with embeddings and sophisticated NounType
taxonomy (30+ entity types) for semantic entity and concept extraction.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/vfs/semantic/projections/AuthorProjection.ts

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+/**
+ * Author Projection Strategy
+ *
+ * Maps author-based paths to files owned by that author
+ * Uses EXISTING MetadataIndexManager for O(log n) queries
+ */
+
+import { Brainy } from '../../../brainy.js'
+import { VirtualFileSystem } from '../../VirtualFileSystem.js'
+import { FindParams } from '../../../types/brainy.types.js'
+import { BaseProjectionStrategy } from '../ProjectionStrategy.js'
+import { VFSEntity } from '../../types.js'
+
+/**
+ * Author Projection: /by-author/<authorName>/<subpath>
+ *
+ * Uses EXISTING infrastructure:
+ * - Brainy.find() with metadata filters (REAL)
+ * - MetadataIndexManager for O(log n) owner queries (REAL)
+ * - VFSMetadata.owner field (REAL - types.ts line 44)
+ */
+export class AuthorProjection extends BaseProjectionStrategy {
+  readonly name = 'author'
+
+  /**
+   * Convert author name to Brainy FindParams
+   */
+  toQuery(authorName: string, subpath?: string): FindParams {
+    const query: FindParams = {
+      where: {
+        vfsType: 'file',
+        owner: authorName
+      },
+      limit: 1000
+    }
+
+    // Filter by filename if subpath specified
+    if (subpath) {
+      query.where = {
+        ...query.where,
+        anyOf: [  // BFO logical operator (not $or)
+          { name: subpath },
+          { path: { endsWith: subpath } }  // BFO operator (not $regex)
+        ]
+      }
+    }
+
+    return query
+  }
+
+  /**
+   * Resolve author to entity IDs using REAL Brainy.find()
+   */
+  async resolve(brain: Brainy, vfs: VirtualFileSystem, authorName: string): Promise<string[]> {
+    // Use REAL Brainy metadata filtering
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        owner: authorName
+      },
+      limit: 1000
+    })
+
+    return this.extractIds(results)
+  }
+
+  /**
+   * List all unique authors
+   * Uses aggregation over metadata
+   */
+  async list(brain: Brainy, vfs: VirtualFileSystem, limit = 100): Promise<VFSEntity[]> {
+    // Get all files with owner metadata
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        owner: { $exists: true }
+      },
+      limit
+    })
+
+    return results.map(r => r.entity as VFSEntity)
+  }
+}

src/vfs/semantic/projections/ConceptProjection.ts

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+/**
+ * Concept Projection Strategy
+ *
+ * Maps concept-based paths to files containing those concepts
+ * Uses EXISTING ConceptSystem and MetadataIndexManager
+ */
+
+import { Brainy } from '../../../brainy.js'
+import { VirtualFileSystem } from '../../VirtualFileSystem.js'
+import { FindParams } from '../../../types/brainy.types.js'
+import { BaseProjectionStrategy } from '../ProjectionStrategy.js'
+import { VFSEntity } from '../../types.js'
+
+/**
+ * Concept Projection: /by-concept/<conceptName>/<subpath>
+ *
+ * Uses EXISTING infrastructure:
+ * - Brainy.find() with metadata filters (REAL - line 580 in brainy.ts)
+ * - MetadataIndexManager for O(log n) concept queries (REAL)
+ * - ConceptSystem for concept extraction (REAL - ConceptSystem.ts)
+ */
+export class ConceptProjection extends BaseProjectionStrategy {
+  readonly name = 'concept'
+
+  /**
+   * Convert concept name to Brainy FindParams
+   * Uses EXISTING FindParams.where for metadata filtering
+   *
+   * Now uses flattened conceptNames array for O(log n) performance!
+   */
+  toQuery(conceptName: string, subpath?: string): FindParams {
+    const query: FindParams = {
+      where: {
+        vfsType: 'file',
+        conceptNames: { contains: conceptName }  // O(log n) indexed query
+      },
+      limit: 1000
+    }
+
+    // If subpath specified, also filter by filename
+    if (subpath) {
+      query.where = {
+        ...query.where,
+        anyOf: [  // BFO logical operator
+          { name: subpath },
+          { path: { endsWith: subpath } }  // BFO operator
+        ]
+      }
+    }
+
+    return query
+  }
+
+  /**
+   * Resolve concept to entity IDs using REAL Brainy.find()
+   * VERIFIED: brain.find() exists at line 580 in brainy.ts
+   *
+   * NOW OPTIMIZED: Uses flattened conceptNames for O(log n) indexed queries!
+   * No more post-filtering - direct index lookup
+   */
+  async resolve(brain: Brainy, vfs: VirtualFileSystem, conceptName: string): Promise<string[]> {
+    // Verify brain.find is a function (safety check)
+    if (typeof brain.find !== 'function') {
+      throw new Error('VERIFICATION FAILED: brain.find is not a function')
+    }
+
+    // Direct O(log n) query using flattened conceptNames array
+    // VFS automatically flattens concepts to conceptNames on write
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        conceptNames: { contains: conceptName }  // Indexed array query
+      },
+      limit: 1000
+    })
+
+    return this.extractIds(results)
+  }
+
+  /**
+   * List all files with concept metadata
+   * Uses REAL Brainy.find() with metadata filter
+   */
+  async list(brain: Brainy, vfs: VirtualFileSystem, limit = 100): Promise<VFSEntity[]> {
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        conceptNames: { exists: true }  // Use flattened field
+      },
+      limit
+    })
+
+    // Convert to VFSEntity array
+    // VERIFIED: Result.entity exists in brainy.types.ts
+    return results.map(r => r.entity as VFSEntity)
+  }
+}

src/vfs/semantic/projections/RelationshipProjection.ts

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+/**
+ * Relationship Projection Strategy
+ *
+ * Maps relationship-based paths to files connected in the knowledge graph
+ * Uses EXISTING GraphAdjacencyIndex for O(1) traversal
+ */
+
+import { Brainy } from '../../../brainy.js'
+import { VirtualFileSystem } from '../../VirtualFileSystem.js'
+import { FindParams } from '../../../types/brainy.types.js'
+import { VerbType } from '../../../types/graphTypes.js'
+import { BaseProjectionStrategy } from '../ProjectionStrategy.js'
+import { RelationshipValue } from '../SemanticPathParser.js'
+
+/**
+ * Relationship Projection: /related-to/<path>/depth-N/types-X,Y
+ *
+ * Uses EXISTING infrastructure:
+ * - Brainy.getRelations() for graph traversal (REAL - line 803 in brainy.ts)
+ * - GraphAdjacencyIndex for O(1) neighbor lookups (REAL)
+ * - VerbType enum for relationship types (REAL - graphTypes.ts)
+ */
+export class RelationshipProjection extends BaseProjectionStrategy {
+  readonly name = 'relationship'
+
+  /**
+   * Convert relationship value to Brainy FindParams
+   * Note: Graph queries don't use FindParams, but we provide this for consistency
+   */
+  toQuery(value: RelationshipValue, subpath?: string): FindParams {
+    // This is informational - actual resolution uses getRelations()
+    return {
+      where: {
+        vfsType: 'file'
+      },
+      connected: {
+        to: value.targetPath,
+        depth: value.depth || 1
+      },
+      limit: 1000
+    }
+  }
+
+  /**
+   * Resolve relationships using REAL Brainy.getRelations()
+   * Uses GraphAdjacencyIndex for O(1) graph traversal
+   */
+  async resolve(brain: Brainy, vfs: VirtualFileSystem, value: RelationshipValue): Promise<string[]> {
+    // Step 1: Resolve target path to entity ID
+    const targetId = await this.resolvePathToId(vfs, value.targetPath)
+    if (!targetId) {
+      return []
+    }
+
+    // Step 2: Get relationships using REAL Brainy graph
+    const depth = value.depth || 1
+    const visited = new Set<string>()
+    const results: string[] = []
+
+    await this.traverseRelationships(
+      brain,
+      targetId,
+      depth,
+      visited,
+      results,
+      value.relationshipTypes
+    )
+
+    // Filter to only files
+    return await this.filterFiles(brain, results)
+  }
+
+  /**
+   * Recursive graph traversal using REAL Brainy.getRelations()
+   */
+  private async traverseRelationships(
+    brain: Brainy,
+    entityId: string,
+    remainingDepth: number,
+    visited: Set<string>,
+    results: string[],
+    types?: string[]
+  ): Promise<void> {
+    if (remainingDepth <= 0 || visited.has(entityId)) {
+      return
+    }
+
+    visited.add(entityId)
+
+    // Get outgoing relationships (REAL method - line 803 in brainy.ts)
+    const relations = await brain.getRelations({
+      from: entityId,
+      limit: 100
+    })
+
+    for (const relation of relations) {
+      // Filter by relationship type if specified
+      if (types && types.length > 0) {
+        const relationshipName = relation.type?.toLowerCase()
+        if (!types.some(t => t.toLowerCase() === relationshipName)) {
+          continue
+        }
+      }
+
+      // Add to results
+      if (!results.includes(relation.to)) {
+        results.push(relation.to)
+      }
+
+      // Recurse if depth remaining
+      if (remainingDepth > 1) {
+        await this.traverseRelationships(
+          brain,
+          relation.to,
+          remainingDepth - 1,
+          visited,
+          results,
+          types
+        )
+      }
+    }
+  }
+
+  /**
+   * Resolve path to entity ID
+   * Helper to convert traditional path to entity ID
+   */
+  private async resolvePathToId(vfs: VirtualFileSystem, path: string): Promise<string | null> {
+    try {
+      // Use REAL VFS public method
+      return await vfs.resolvePath(path)
+    } catch {
+      return null
+    }
+  }
+}

src/vfs/semantic/projections/SimilarityProjection.ts

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+/**
+ * Similarity Projection Strategy
+ *
+ * Maps similarity-based paths to files with similar content
+ * Uses EXISTING HNSW Index for O(log n) vector similarity
+ */
+
+import { Brainy } from '../../../brainy.js'
+import { VirtualFileSystem } from '../../VirtualFileSystem.js'
+import { FindParams } from '../../../types/brainy.types.js'
+import { BaseProjectionStrategy } from '../ProjectionStrategy.js'
+import { SimilarityValue } from '../SemanticPathParser.js'
+
+/**
+ * Similarity Projection: /similar-to/<path>/threshold-N
+ *
+ * Uses EXISTING infrastructure:
+ * - Brainy.similar() for vector similarity (REAL - line 680 in brainy.ts)
+ * - HNSW Index for O(log n) nearest neighbor search (REAL)
+ * - Cosine similarity for scoring (REAL)
+ */
+export class SimilarityProjection extends BaseProjectionStrategy {
+  readonly name = 'similar'
+
+  /**
+   * Convert similarity value to Brainy FindParams
+   * Note: Similarity uses brain.similar(), not find(), but we provide this for consistency
+   */
+  toQuery(value: SimilarityValue, subpath?: string): FindParams {
+    // This is informational - actual resolution uses brain.similar()
+    return {
+      where: {
+        vfsType: 'file'
+      },
+      near: {
+        id: value.targetPath,
+        threshold: value.threshold || 0.7
+      },
+      limit: 50
+    }
+  }
+
+  /**
+   * Resolve similarity using REAL Brainy.similar()
+   * Uses HNSW Index for O(log n) vector search
+   */
+  async resolve(brain: Brainy, vfs: VirtualFileSystem, value: SimilarityValue): Promise<string[]> {
+    // Step 1: Resolve target path to entity ID
+    const targetId = await this.resolvePathToId(vfs, value.targetPath)
+    if (!targetId) {
+      return []
+    }
+
+    // Step 2: Get target entity to use its vector
+    const targetEntity = await brain.get(targetId)
+    if (!targetEntity) {
+      return []
+    }
+
+    // Step 3: Find similar entities using REAL HNSW search
+    // VERIFIED: brain.similar() exists at line 680 in brainy.ts
+    const results = await brain.similar({
+      to: targetEntity,
+      threshold: value.threshold || 0.7,
+      limit: 50,
+      where: { vfsType: 'file' }  // Only files
+    })
+
+    // Extract IDs
+    return this.extractIds(results)
+  }
+
+  /**
+   * Resolve path to entity ID
+   */
+  private async resolvePathToId(vfs: VirtualFileSystem, path: string): Promise<string | null> {
+    try {
+      // Use REAL VFS public method
+      return await vfs.resolvePath(path)
+    } catch {
+      return null
+    }
+  }
+}

src/vfs/semantic/projections/TagProjection.ts

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+/**
+ * Tag Projection Strategy
+ *
+ * Maps tag-based paths to files with those tags
+ * Uses EXISTING MetadataIndexManager for O(log n) queries
+ */
+
+import { Brainy } from '../../../brainy.js'
+import { VirtualFileSystem } from '../../VirtualFileSystem.js'
+import { FindParams } from '../../../types/brainy.types.js'
+import { BaseProjectionStrategy } from '../ProjectionStrategy.js'
+import { VFSEntity } from '../../types.js'
+
+/**
+ * Tag Projection: /by-tag/<tagName>/<subpath>
+ *
+ * Uses EXISTING infrastructure:
+ * - Brainy.find() with metadata filters (REAL)
+ * - MetadataIndexManager for O(log n) tag queries (REAL)
+ * - VFSMetadata.tags field (REAL - types.ts line 66)
+ */
+export class TagProjection extends BaseProjectionStrategy {
+  readonly name = 'tag'
+
+  /**
+   * Convert tag name to Brainy FindParams
+   */
+  toQuery(tagName: string, subpath?: string): FindParams {
+    const query: FindParams = {
+      where: {
+        vfsType: 'file',
+        tags: { contains: tagName }  // BFO operator for array contains
+      },
+      limit: 1000
+    }
+
+    // Filter by filename if subpath specified
+    if (subpath) {
+      query.where = {
+        ...query.where,
+        anyOf: [  // BFO logical operator
+          { name: subpath },
+          { path: { endsWith: subpath } }  // BFO operator
+        ]
+      }
+    }
+
+    return query
+  }
+
+  /**
+   * Resolve tag to entity IDs using REAL Brainy.find()
+   */
+  async resolve(brain: Brainy, vfs: VirtualFileSystem, tagName: string): Promise<string[]> {
+    // Use REAL Brainy metadata filtering
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        tags: { contains: tagName }  // BFO operator
+      },
+      limit: 1000
+    })
+
+    return this.extractIds(results)
+  }
+
+  /**
+   * List all files with tags
+   */
+  async list(brain: Brainy, vfs: VirtualFileSystem, limit = 100): Promise<VFSEntity[]> {
+    // Get all files that have tags
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        tags: { exists: true }  // BFO operator
+      },
+      limit
+    })
+
+    return results.map(r => r.entity as VFSEntity)
+  }
+}

src/vfs/semantic/projections/TemporalProjection.ts

@@ -0,0 +1,103 @@
+/**
+ * Temporal Projection Strategy
+ *
+ * Maps time-based paths to files modified at that time
+ * Uses EXISTING MetadataIndexManager with range queries
+ */
+
+import { Brainy } from '../../../brainy.js'
+import { VirtualFileSystem } from '../../VirtualFileSystem.js'
+import { FindParams } from '../../../types/brainy.types.js'
+import { BaseProjectionStrategy } from '../ProjectionStrategy.js'
+import { VFSEntity } from '../../types.js'
+
+/**
+ * Temporal Projection: /as-of/<YYYY-MM-DD>/<subpath>
+ *
+ * Uses EXISTING infrastructure:
+ * - Brainy.find() with range queries (REAL)
+ * - MetadataIndexManager.$gte/$lte operators (REAL)
+ * - VFSMetadata.modified field (REAL - types.ts line 49)
+ */
+export class TemporalProjection extends BaseProjectionStrategy {
+  readonly name = 'time'
+
+  /**
+   * Convert date to Brainy FindParams with range query
+   */
+  toQuery(date: Date, subpath?: string): FindParams {
+    // Get start and end of day (24-hour window)
+    const startOfDay = new Date(date)
+    startOfDay.setHours(0, 0, 0, 0)
+
+    const endOfDay = new Date(date)
+    endOfDay.setHours(23, 59, 59, 999)
+
+    const query: FindParams = {
+      where: {
+        vfsType: 'file',
+        modified: {
+          greaterEqual: startOfDay.getTime(),  // BFO operator
+          lessEqual: endOfDay.getTime()        // BFO operator
+        }
+      },
+      limit: 1000
+    }
+
+    // Filter by filename if subpath specified
+    if (subpath) {
+      query.where = {
+        ...query.where,
+        anyOf: [  // BFO logical operator (not $or)
+          { name: subpath },
+          { path: { endsWith: subpath } }  // BFO operator (not $regex)
+        ]
+      }
+    }
+
+    return query
+  }
+
+  /**
+   * Resolve date to entity IDs using REAL Brainy.find()
+   * Uses MetadataIndexManager range queries for O(log n) performance
+   */
+  async resolve(brain: Brainy, vfs: VirtualFileSystem, date: Date): Promise<string[]> {
+    const startOfDay = new Date(date)
+    startOfDay.setHours(0, 0, 0, 0)
+
+    const endOfDay = new Date(date)
+    endOfDay.setHours(23, 59, 59, 999)
+
+    // Use REAL Brainy metadata filtering with range operators
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        modified: {
+          greaterEqual: startOfDay.getTime(),  // BFO operator
+          lessEqual: endOfDay.getTime()        // BFO operator
+        }
+      },
+      limit: 1000
+    })
+
+    return this.extractIds(results)
+  }
+
+  /**
+   * List recently modified files
+   */
+  async list(brain: Brainy, vfs: VirtualFileSystem, limit = 100): Promise<VFSEntity[]> {
+    const oneDayAgo = Date.now() - (24 * 60 * 60 * 1000)
+
+    const results = await brain.find({
+      where: {
+        vfsType: 'file',
+        modified: { greaterEqual: oneDayAgo }  // BFO operator
+      },
+      limit
+    })
+
+    return results.map(r => r.entity as VFSEntity)
+  }
+}