Top down default use internal ions

[trishorts]

Propose "Use Internal Ions" = true
"Min Internal Ion Length" = 10
for top-down search in default toml.

In the large Jurkat dataset with xml we got the following results with default toml:

All target PSMs with q-value <= 0.01: 41719
All target proteoforms with q-value <= 0.01: 3082
All target protein groups with q-value <= 0.01 (1% FDR): 209

Using internal ions gave the following:

All target PSMs with q-value <= 0.01: 39437
All target proteoforms with q-value <= 0.01: 5958
All target protein groups with q-value <= 0.01 (1% FDR): 145