- After Govardana Hill incident, did Indra know that Krishna was Incarnation of Lord Vishnu?
- If He knew Krishna as Avatar of Lord Vishnu after that incident, why did Indra fight with Krishna when Krishna stole Parijata flowers from Amaravati, abode of Indra?
- Indra helped Arjuna many times as Arjuna was his son. At the same time Krishna and Arjuna were best friends. So how were Indra and Krishna? Were they hostile or were they friendly?
About why Indra fought for Parijata tree there's shloka in Bhagavata-purana, 10.59.41, directly after short shloka about Parijata tree:
yayāca ānamya kirīṭa-koṭibhih ̣ pādau spṛśann acyutam artha-sādhanam siddhārtha etena vigṛhyate mahān aho surāṇāḿ ca tamo dhig āḍhyatām
ISKCON translation (you can use whatever you prefer, it'll not change anything serious):
Even after Indra had bowed down to Lord Acyuta, touched His feet with the tips of his crown and begged the Lord to fulfill his desire, that exalted demigod, having achieved his purpose, chose to fight with the Supreme Lord. What ignorance there is among the gods! To hell with their opulence!
About your first question, in the same Bhagavata-purana, 10.27.5, right after the story about Govardhana hill, Indra calls Krishna not just an "avatar of Vishnu", but the Bhagavan, meaning, in short, Supreme God.
Both stories described rather succinctly in Bhagavatam, by the way. No specific details about someone's words or preferences.
Indira, the king of heaven did not attack Krishna on his own thought, but he fought with him because his wife Saci complained him which may be due to some jealousness she had towards Satyabhama, Krishna's wife.Those who listens to the advice of their wives and have no sense of conscience are definitely fools and the similar thing happened with Indira.So his mind not steady and puzzled, he was not able to decide on his own and went to fight with Krishna who himself is the god.