no gap-filling in "scaffold" mode?

Hi again!

I have now run dentist successfully a few times and tested the different join policies, using as input the raw contig assembly or a scaffold assembly, scaffolded with `LRscaf`.

I get the best N50 running dentist with `join-policy: scaffolds` on the already scaffolded assembly (13.5 Mb). However, the final `gap-closed.fasta` contains almost as many `N`s (186183) as the input assembly `reference.fasta` (186185).

When running with `join-policy: contigs`, neither the reference.fasta nor the gap-closed.fasta contain any `N`s.

Is it intended that gaps are not closed in the `join-policy:scaffold`-mode? Do I have to run dentist a second time with `join-policy: scaffoldGaps` to actually glose the gaps in the 13.5 Mb assembly?

As far as I can tell, all dentist runs finished without any errors.

Here are some stats of the different assemblies:

### `join-policy: scaffolds`
```
file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%)
gap-closed.fasta FASTA DNA 117 340,348,369 1,843 2,908,960.4 28,227,288 9,395 77,974 2,243,295 0 13,556,940 0 0
reference.fasta FASTA DNA 122 340,337,486 940 2,789,651.5 28,227,288 8,609 89,797 2,243,295 0 12,859,076 0 0
```

### `join-policy: contigs`
```
file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%)
gap-closed.fasta FASTA DNA 161 303,401,106 1,069 1,884,478.9 28,227,288 7,516 31,549 988,561 0 10,239,100 0 0
reference.fasta FASTA DNA 171 303,403,113 520 1,774,287.2 25,232,339 7,314 31,549 971,039.5 0 9,931,962 0 0
```

The issue is about gap-filling behavior in 'scaffold' mode. Examine the join-policy logic in the codebase, likely in a main processing module or configuration handler. Look for the 'scaffold' and 'scaffoldGaps' modes to understand the gap-closing flow. Run tests with scaffolded input to reproduce the N-count issue and verify if gaps are being processed.

Written by the indexing model from the issue text.