This all files were synced to repository after project creation.
As components needs to be developed in sightly, I opened ui.apps project folder in brackets after installing sightly plugin and applied project settings for localhost along with username and password .
Now if I edit and save any component .html file of myapp in brackets, it deletes all nodes below /apps/myapp, also it deletes current component .html file that is saved.
Only nodes that remains are the nodes till the path to current component node.
Appreciate if any one can help to resolve this issue.
You need to open the folder that contains the jcr_root folder (as well as the META-INF folder). In the case of projects created with the "AEM Sample Multi-Module Project" archetype, like the Eclipse plugin does, then you have to open ui.apps/src/main/content in Brackets.
If you don't open the right folder, then the synchronization of your content within Brackets with your AEM instance doesn't work.