refactor: optimize database performance with new indexes

This commit introduces new SQL migration files to create indexes that enhance query performance for protocol components.

Author: zizou0x

tycho-storage/migrations/2025-07-21_index_protocol_components/down.sql

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+DROP INDEX IF EXISTS idx_protocol_system_id_external_id;
+DROP INDEX IF EXISTS idx_protocol_component_system_id;

tycho-storage/migrations/2025-07-21_index_protocol_components/notes.md

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+# Database Query Optimizations
+
+## 1. EntryPoint Query Optimization
+
+- **Purpose**: Speed up lookup queries on `(protocol_system_id, external_id)` for EntryPoint resolution.
+- **Initial Execution Time**: 130ms
+- **Optimized Execution Time**: 0.1ms
+
+**Index Added:**
+
+```sql
+CREATE INDEX IF NOT EXISTS idx_protocol_system_id_external_id ON protocol_component (protocol_system_id, external_id);
+```
+
+## 1. ProtocolComponent count Query Optimization
+
+- **Purpose**: Improve efficiency of count queries (e.g., for pagination) by filtering on protocol_system_id.
+- **Initial Execution Time**: 100ms
+- **Optimized Execution Time**: 50ms
+
+**Index Added:**
+
+```sql
+CREATE INDEX idx_protocol_component_system_id ON protocol_component (protocol_system_id);
+```

tycho-storage/migrations/2025-07-21_index_protocol_components/up.sql

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+CREATE INDEX IF NOT EXISTS idx_protocol_system_id_external_id ON protocol_component (protocol_system_id, external_id);
+CREATE INDEX idx_protocol_component_system_id ON protocol_component (protocol_system_id);