Add freshness scoring, auto-decay, and USAGE.md

Add lastAccessedAt timestamp to nodes with schema migration and
backfill. Touch timestamp on read, apply exponential freshness decay
(~69-day half-life) to search scoring alongside BM25 and vector
weights. Add auto-decay that marks untouched nodes as stale after a
configurable threshold, with CLI command and server-side daily interval.
Include comprehensive USAGE.md documenting all CLI commands and REST API.

src/core/db.ts

@@ -61,6 +61,13 @@ export function getDb(): Database.Database {
   _db.pragma('foreign_keys = ON');
   _db.exec(SCHEMA);
 
+  // Migration: add last_accessed_at column
+  const cols = _db.prepare("PRAGMA table_info(nodes)").all() as any[];
+  if (!cols.some((c: any) => c.name === 'last_accessed_at')) {
+    _db.exec('ALTER TABLE nodes ADD COLUMN last_accessed_at INTEGER');
+    _db.exec('UPDATE nodes SET last_accessed_at = updated_at WHERE last_accessed_at IS NULL');
+  }
+
   return _db;
 }