Add ability to restart a failed project with `matchids` option

In some cases, the forward and reverse read files don't match exactly, apparently because they were filtered separately. The DADA2 [matchids](https://benjjneb.github.io/dada2/faq.html) option will attempt to pair them up. It'd be nice if we had a way to restart a project with `matchids` enabled, in situations where there are a practical number of reverse reads and it'd be better than just re-running as single-end.

My first guess is by adding optional flags to the `again` command.

Example from project PRJNA639644:
```
Loading required package: Rcpp
Read 227 items
[1] "Thu Jan 12 21:11:08 2023 Paired-end data found!"
[1] "Thu Jan 12 21:11:08 2023 Filtering..."
Error in filterAndTrim(forward_reads, filtered_forward_reads, reverse_reads, :
These are the errors (up to 5) encountered in individual cores...
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 39797, 39795.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 47109, 47108.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 7700, 7696.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 39797, 39795.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 47109, 47108.
In addition: Warning message:
In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule, :
scheduled cores 1, 5, 7 encountered errors in user code, all values of the jobs will be affected
Execution halted
```