Add support of alignment rules

[lukfor]

This pull request adds the following:

• a property alignmentRules to tree.yaml and applies them on each fasta file import.
• a flag --skip-alignment-rules to the command-line version to disable them
• reads the hotspots from tree.yaml

To discuss:

• [x] Webservice applies rules on every fasta file. Should we add checkbox to disable alignment rules manually? @seppinho