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the initial vault sync version (up to 2.4.24) just sync simple folders and files and ignores vault serialized files (.content.xml, .dialog.xml, etc...) so that you can use it in combination with vlt command line tool.
Just so I'm clear - the development process would be:
1) Checkout using vlt co
2) Set up the sync - so that the JSPs you work with don't have to be manually checked in
3) Use vlt ci to make changes to any of the serialized files.
it depends where your content first comes from (vcs or your local repository), but i would rather say, once all is set up :
* for serialized files (nodes) that often needs less dev. you do either vlt co / vlt ci depending on where you change the content
* for files (jsp, js, css) in which will 90% of your dev, just have sync enabled so that you code within your IDE and it's seemless.