### 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

fix: issue https://github.com/infiniflow/ragflow/issues/5600

### What problem does this PR solve?

close issue https://github.com/infiniflow/ragflow/issues/5600 

### Type of change

- [x] Bug Fix (non-breaking change which fixes an issue)

### 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?

#4180

### Type of change

- [x] Bug Fix (non-breaking change which fixes an issue)

### What problem does this PR solve?

Fix errors detected by Ruff

### Type of change

- [x] Refactoring

### What problem does this PR solve?

leiden alg throws exception for lack func cast definition

### Type of change

- Bug Fix (non-breaking change which fixes an issue)

### What problem does this PR solve?

Introduced [beartype](https://github.com/beartype/beartype) for runtime
type-checking.

### Type of change

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

### What problem does this PR solve?

Use consistent log file names, introduced initLogger

### Type of change

- [ ] Bug Fix (non-breaking change which fixes an issue)
- [ ] New Feature (non-breaking change which adds functionality)
- [ ] Documentation Update
- [x] Refactoring
- [ ] Performance Improvement
- [ ] Other (please describe):

### What problem does this PR solve?

- remove repeat func

### Type of change

- [x] Other (please describe): remove repeat func

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

### What problem does this PR solve?


### Type of change

- [x] Bug Fix (non-breaking change which fixes an issue)

### What problem does this PR solve?

#1594

### Type of change

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