Check E004 once per file, not once per invocation

[taowang487]

The last line should always end with a newline check sits at the same indent level as the for fname in files loop, so it runs a single time after every file has been processed, against the line variable left over from whichever file was scanned last. Files earlier in the list are never checked.

bashate a.sh b.sh   # a.sh missing its newline -> not reported
bashate b.sh a.sh   # same a.sh                -> reported

This inverts a 2016 regression. Before
I54963cd25efc9f9603fbcc60b8e25bb11ea2d7db the check lived in the isfirstline() block and, as that commit noted, could not fire unless you passed two files; the fix moved it out of the loop but dedented one level too far, so now it cannot fire unless the file is passed last. The test added at the same time is single-file, so it passes under both behaviours.

Move the check inside the per-file loop and track the file's last raw line separately -- line is unusable here because it is rewritten by inline-comment stripping and rebound by the for line in logical_line loop. filename/filelineno are passed explicitly since fileinput is exhausted by that point.

Callers that batch files into one invocation, such as pre-commit, are most affected: the same offending file passes or fails depending only on how the file list happens to be ordered.