Options from plugins not processed in Application#bootstrap

[rbuckton]

In #610 a change was made to Application#bootstrap. In this change, the argument to this.options.read was changed from options to this.options.getRawValues(), however getRawValues only returns the options that were already successfully parsed. At the point those options were parsed, plugins had not yet been loaded (since they depend on Prefetch), so custom options added by plugins are ignored if they are passed as part of the options object.

While this doesn't negatively impact parsing CLI arguments, it means that custom options passed to gulp-typescript are not parsed correctly.

[NeKJ]

I agree, this is a regression for plugins that work with gulp-typedoc and should be fixed. I am afraid it is not easy though as the fix for the CLI case should be kept but find a workaround to make this work gulp-typedoc too. Maybe if the setValue() of Options, added the values regardless if they were declared or not, so the getRawValues() will return all passed-in values and on the second call will be able to retrieve the values of the declared options from plugins?

[Gerrit0]

This has now been fixed, see #1016. Will be released in v0.16.0