I don't understand how ignoring version in the VFS help us here🤔

Because cabal only works with the physical file system. If the VFS changes, then cabal simply can't perform a reload, as cabal repl will still observe the same .cabal file. That's why we only want to invalidate the shake session, if the .cabal file on disk has been modified.

Further, let's have a look at getModificationTimeImpl:

getModificationTimeImpl
 :: Bool
 -> NormalizedFilePath
 -> Action (Maybe BS.ByteString, ([FileDiagnostic], Maybe FileVersion))
getModificationTimeImpl missingFileDiags file = do
 let file' = fromNormalizedFilePath file
 let wrap time = (Just $ LBS.toStrict $ B.encode $ toRational time, ([], Just $ ModificationTime time))
 mbVf <- getVirtualFile file
 case mbVf of
 Just (virtualFileVersion -> ver) -> do
 alwaysRerun
 pure (Just $ LBS.toStrict $ B.encode ver, ([], Just $ VFSVersion ver))
 Nothing -> do
 isWF <- use_ AddWatchedFile file
 if isWF
 then -- the file is watched so we can rely on FileWatched notifications,
 -- but also need a dependency on IsFileOfInterest to reinstall
 -- alwaysRerun when the file becomes VFS
 void (use_ IsFileOfInterest file)
 else if isInterface file
 then -- interface files are tracked specially using the closed world assumption
 pure ()
 else -- in all other cases we will need to freshly check the file system
 alwaysRerun
 
 ...

First, we don't care about the isInterface file check. Then, if the file isn't open in the VFS, we will never rerun this rule, unless the IsFileOfInterest rule is marked dirty, which it never will for .cabal files.

In my understanding, isWF will be True for .cabal files.

Thanks for the explanation, much clear to me now.

If I am not mistaken, GetPhysicalModificationTime is for .cabal files?
and cfps' are mostly .hs file locations, and we are type checking those files here.

But I do not really know how we handle .cabal file in HLS and where we call GetModificationTime for .cabal files.

Good catch, this is wrong, it should be GetModificationTime