I'm using drupal commerce with its submodules and need to change order's confirmation message to html format and add line items and customer profile. How can I organize this?
Use Commerce Message. It's the best supported way to handle sending emails. It includes several message types out of the box.
If HTML emails are a requirement, check out the Commerce Invoice Receipt module. Here's an excerpt from the project page:
Provides an additional 'Invoice' display for Commerce orders, as well as a Rules action to email this invoice out to customers.
The HTML email can be customised through template files.