Well in Haskell there are 2 main ways of parsing something, parse combinators or a parser generator. Since you already have a BNF I'd suggest the latter.
A good one is alex. GHC's parser IIRC is written using this so you'd be in good company.
Next you'll have a big honking stack of data declarations to parse into:
data JavaClass = {
className :: Name,
interfaces :: [Name],
contents :: [ClassContents],
...
}
data ClassContents = M Method
| F Field
| IC InnerClass
and for expressions and whatever else you need. Finally you'll combine these into something like
data TopLevel = JC JavaClass
| WhateverOtherForms
| YouWillParse
Once you have this you'll have the entire AST represented as one TopLevel or a list of them depending on how many you classes/files you parse.
To proceed from here depends on what you want to do. There are a number of libraries such as syb (scrap your boilerplate) that let you write very concise tree traversals and modifications. lens is also an option. At a minimum check out Data.Traversable and Data.Foldable.
To modify the tree, you can do something as simple as
ignoreInnerClasses :: JavaClass -> JavaClass
ignoreInnerContents c = c{contents = filter isClass $ contents c}
-- ^^^ that is called a record update
where isClass (IC _) = True
isClass _ = False
and then you could potentially use something like syb to write
everywhere (mkT ignoreInnerClass) toplevel
which will traverse everything and apply ignoreInnerClass to all JavaClasses. This is possible to do in lens and many other libraries too, but syb is very easy to read.
