Fix --out_filtered_bam <file> creating a directory for a single BAM (2.1.1)

[ishinder]

Summary

A bare single-file --out_filtered_bam (e.g. --out_filtered_bam filtered.bam) created a directory filtered.bam/ and wrote the filtered BAM inside it, instead of writing the file. 2.1.0 fixed OutputWriter::generate_bam_output_paths, but two inline sites in main.cpp run first and create the directory — which then flips is_file_path (it checks fs::is_directory) into directory mode, defeating the 2.1.0 fix:

• the auto-built bowtie2 index directory (main.cpp:340-342 → fs::create_directories in build_bowtie2_index), and
• the temporary spurious-junction BED directory (main.cpp:514-516).

Both used the anti-pattern "if parent_path() is empty, use the output path itself as a directory."

Fix

Two pure, unit-testable helpers in path_utils that never treat a single output file as a directory:

• index_output_dir() — bare filename → "" so the index builds in its own <reference>_bt2_idx/ directory next to the reference FASTA (the existing default), not in a dir named after the file.
• sidecar_dir() — bare filename → "." so the temp BED has a concrete directory without creating one named after the file.

main.cpp now calls these. The temp BED name is also made pid-unique to avoid collisions between concurrent runs sharing an output directory.

Net effect: nothing creates filtered.bam/; a bare single-file --out_filtered_bam writes that file (and --removed_alignments_bam writes <name>_removed_alignments.bam beside it), with no stray directory. Directory mode for BAM lists is unchanged.

Tests / verification

• New regression unit tests for index_output_dir / sidecar_dir and the single-BAM+directory case (tests/test_path_utils.cpp).
• Verified end-to-end against the real binary on a synthesized BAM: bare filename (with and without -i), --removed_alignments_bam, single→directory, and a 2-BAM list→directory. All produce the expected files with no stray directory.

Docs / version

• README documents where the auto-built index lives + read-only-reference caveat.
• CHANGELOG: honest 2.1.1 entry; corrects the stale 2.1.0 "unreleased" header and softens its --out_filtered_bam over-claim.
• Version bumped to 2.1.1 (CMakeLists + conda/meta.yaml).