go.tools/godoc: remove nil deference panic on loading error
go.tools/godoc: remove nil deference panic on loading error

Also:
- remove stale comment about line numbers.
- log a warning if file's package root not found.

LGTM=bgarcia
R=bgarcia
CC=golang-codereviews
https://codereview.appspot.com/88510044

karmakaze/go.tools,chenjianlong/go.tools,chenjianlong/go.tools,karmakaze/go.tools,chenjianlong/go.tools,karmakaze/go.tools,karmakaze/go.tools,karmakaze/go.tools