[Chore/Refactor] db.session.xxx -> with Session as session

[asukaminato0721]

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Description

db.session.commit() is Flask-SQLAlchemy

with Session(...) is Pure SQLAlchemy

Motivation

for migration.

Additional Context

https://docs.sqlalchemy.org/en/20/orm/session_basics.html#framing-out-a-begin-commit-rollback-block

part of COM-7832

need facebook/pyrefly#954

one example: #24135

[liugddx]

I will try

[laipz8200]

It seems this hasn't changed anything?

[asukaminato0721]

It seems this hasn't changed anything?

prepare for #24138

[ruanimal]

why use Pure SQLAlchemy ？

[asukaminato0721]

why use Pure SQLAlchemy ？

#10921 (comment)

[asukaminato0721]

still some remaining places.