Remove deprecated file system APIs

[peterflynn]

We shouldn't fix this any sooner than Sprint 36.

Remove all the APIs listed at https://github.com/adobe/brackets/wiki/File-System-API-Migration#deprecated-apis, including:

• Remove NativeFileSystem module
• Remove FileIndexManager module
• Remove NativeFileError module

We should do one more double-check for extensions referencing these modules so we know how many, if any, will be broken before committing to making this change in a particular sprint.

[peterflynn]

We should probably do this simple API cleanup before 1.0 -- nominating

[redmunds]

According to semantic versioning, All deprecated API should be removed before 1.0, right? Should we expand the scope of this issue, or should I file another one? I guess this really needs to be a Trello card.

[peterflynn]

Closing since #8751 is a superset of this