### What problem does this PR solve?

Removed set_entity and set_relation to avoid accessing doc engine during
graph computation.
Introduced GraphChange to avoid writing unchanged chunks.

### Type of change

- [x] Performance Improvement

### What problem does this PR solve?

#4543

### Type of change

- [x] New Feature (non-breaking change which adds functionality)

### What problem does this PR solve?

### Type of change

- [x] Refactoring

Signed-off-by: Jin Hai <haijin.chn@gmail.com>

### What problem does this PR solve?

#1594

### Type of change

- [x] New Feature (non-breaking change which adds functionality)