feat: Add database schema for document-aware chunking (Phase 1)

This commit introduces the foundational schema and types needed to support
document chunking while maintaining backward compatibility with existing data.

Schema Changes:
- Added `is_chunk`, `parent_document_id`, `chunk_order` columns to nodes table
- Added `edge_type` column to edges table (semantic, parent-child, sequential, manual)
- All new columns have appropriate defaults for backward compatibility

Type Updates:
- NodeRecord now includes chunking metadata fields
- EdgeRecord now includes edgeType discriminator
- Created parseNodeRow() and parseEdgeRow() helper functions

Core Infrastructure:
- src/core/import.ts - Document import with chunking and structural edges
- src/lib/chunking.ts - Header-based and size-based chunking strategies

Updated all edge/node creation sites to include new required fields:
- Semantic edges marked as 'semantic' (auto-linking)
- Manual edges marked as 'manual' (user-created links)
- Parent-child edges marked as 'parent-child' (document structure)
- Sequential edges marked as 'sequential' (chunk ordering)
- All nodes marked with isChunk=false unless explicitly chunked

Next phases will add:
- Document reconstruction utilities
- UX updates to hide chunks and show parent documents
- forest import command for explicit document ingestion

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

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

Author: bwl

src/cli/commands/admin-recompute-embeddings.ts

@@ -90,6 +90,7 @@ async function runAdminRecomputeEmbeddings(flags: AdminRecomputeEmbeddingsFlags)
         targetId,
         score,
         status: status as EdgeStatus,
+        edgeType: 'semantic',
         metadata: { components },
         createdAt: new Date().toISOString(),
         updatedAt: new Date().toISOString(),

src/cli/commands/capture.ts

@@ -130,6 +130,9 @@ async function runCapture(flags: CaptureFlags) {
     embedding,
     createdAt: new Date().toISOString(),
     updatedAt: new Date().toISOString(),
+    isChunk: false,
+    parentDocumentId: null,
+    chunkOrder: null,
   };
 
   const existingNodes = await listNodes();

src/cli/commands/edges.ts

@@ -769,6 +769,7 @@ async function runEdgesUndo(ref: string | undefined) {
       targetId,
       score: (event.payload?.score as number) ?? 0,
       status: 'suggested',
+      edgeType: 'semantic',
       metadata: event.payload?.metadata ?? null,
       createdAt: new Date().toISOString(),
       updatedAt: new Date().toISOString(),
@@ -786,6 +787,7 @@ async function runEdgesUndo(ref: string | undefined) {
       targetId,
       score: (event.payload?.score as number) ?? 0,
       status: 'suggested',
+      edgeType: 'semantic',
       metadata: event.payload?.metadata ?? null,
       createdAt: new Date().toISOString(),
       updatedAt: new Date().toISOString(),