Exclude unmapped calls from CpG summaries

[SuhasSrinivasan]

Fixes #649.

Summary

• exclude unmapped records from indexed summary --cpg results, matching the documented --motif CG 0 behavior
• add an end-to-end CLI regression with a valid unmapped MM/ML/MN record

Root cause and impact

The indexed summary path correctly constructs a CG motif for --cpg, but the later guard that skips unmapped-record collection checked only mapped_only, matched_only, and an explicit motif. Because the CpG shorthand flag was omitted, all unmapped modification calls were merged into the mapped reference-CpG histogram.

On the mapped-plus-unmapped fixture from #649, modkit 0.6.4 reports 20 reads and 186 C calls under --cpg, versus 10 reads and 77 calls under --motif CG 0. With this change, both forms report the same scientific counts.

Regression

The test copies the existing 10 mapped test records and appends an unmapped CCCC record with:

• MM:Z:C+m?,0,0,0,0;
• four ML values of 255
• MN:i:4

It runs the actual CLI, normalizes TSV key/value ordering, and requires the mixed result to equal the mapped-only control with total_reads_used=10, count_reads_C=10, and C_total_mod_calls=77.

Validation

• confirmed the finalized regression fails on the parent revision: total_reads_used is 11 instead of 10
• cargo test -p modkit --test test_summary test_summary_cpg_excludes_unmapped_calls -- --exact
• cargo test -p modkit --test test_summary (5 passed)
• cargo test -p modkit --test test_pileup -- --test-threads=1 (16 passed, 10 ignored)
• cargo test --workspace --quiet -- --test-threads=1
• rustfmt --check --edition 2021 modkit-core/src/modbam_util/subcommands.rs modkit/tests/test_summary.rs
• git diff --check
• installed-versus-patched CLI comparison on the issue fixture: 20 / 186 becomes 10 / 77 and matches explicit --motif CG 0

An initial default-parallel package run exposed an existing integration-test collision: test_pileup_no_filt and test_pileup_with_header both write /tmp/test_pileup_nofilt.bed. The pileup target and full workspace pass when run serially; this branch does not touch pileup.