packages/hardhat/contracts is where you will add and edit your smart contracts. deploy is where your main deploy script lives. When you create a new smart contract this is where you will reference it in order to deploy it the network specified in hardhat.config.js. scripts is where you might keep your helper scripts, such as publish.js which publishes a specified subgraph to The Graph. Or you might have a script to mint a series of NFTs.
test is where you will keep your test suite for your smart contracts. hardhat.config.js is where you will specify the network to deploy your smart contracts to on yarn deploy, provide Infura keys for each network, specify your desired solidity compiler versions, etc. package.json is where your dependencies and npm scripts are specified.
Please read the Hardhat docs in order to get a full understanding of these directories and their contents.