Short read aligners: incorrect index processing

When UGENE-3823 was fixed short read aligners became incorrect. They does not process index files correctly. For example:
1. Open the "Align Sequencing Read" dialog.
2. Choose Bowtie.
3. Set a Bowtie index (*.1.ebwt) file as a reference sequence.
4. Choose a reads file.
5. Click "Start".
Actual: UGENE tell that the reference sequence file has unknown format.

For reusing prebuilt index UGENE requires that index files are located in the same directory as a source FASTA and you have to choose the FASTA in the dialog. It's totally incorrect because aligners don't require the source FASTA for aligning and users even may not have the source FASTA.

Make aligners behavior the following:
1. They must work when you set a FASTA without an index file as a reference. Index is built in the same directory in this case.
2. They must work when you set an index file as a reference.
3. They must work when you set a FASTA with index files in the same directory as a reference. The index is reused in this case.
4. The same behavior must be in Workflow Designer.