fix(output): move pass-1 SJ tab into <prefix>_STARpass1/SJ.out.tab

[pinin4fjords]

Summary

STAR keeps two-pass intermediates inside <prefix>_STARpass1/ with the pass-1 splice tab named SJ.out.tab inside that directory. rustar was emitting it as <prefix>SJ.pass1.out.tab at the top level. This PR moves the file to the STAR-equivalent location.

The file content is unchanged — only the path moves. The <prefix>_STARpass1/ directory is create_dir_all'd before the write.

Scope (changed during review)

Initial scope of this PR also added minimal-stub writers for Log.out and Log.progress.out. Those have been reverted in the latest commit: writing files that mimic STAR's section-header structure with placeholder content (a Debug-format params dump, three timestamps) closes the file-existence gap but misleads downstream tools that try to parse memory usage, per-chunk progress, or warnings out of Log.out. Real parity for those two files is a separate engineering effort — periodic per-chunk updates during long runs, warnings, the full STAR parameter format. Tracked as a follow-up; not stubbed here.

So this PR now only addresses the SJ.pass1.out.tab placement (the second bullet of #28). The Log.out / Log.progress.out bullet stays open on that issue.

Test plan

• Integration test asserts <prefix>_STARpass1/SJ.out.tab exists after a --twopassMode Basic run
• Integration test asserts top-level <prefix>SJ.pass1.out.tab does NOT exist
• cargo build
• cargo clippy --lib -- -D warnings
• cargo fmt --check
• cargo test --lib (383 pass) + cargo test --test alignment_features test_two_pass_mode (pass)

Refs #28 (placement half only; Log.out / Log.progress.out parity is a follow-up)

[pinin4fjords]

Verified end-to-end on macOS/aarch64 against the rebuilt fix branch (commit e91433a — stubs reverted, placement-only).

PE yeast + --twopassMode Basic:

$ ls V28v2./
Aligned.out.bam
Log.final.out
SJ.out.tab
_STARpass1

$ ls V28v2./_STARpass1/
SJ.out.tab

$ [ -f V28v2./SJ.pass1.out.tab ] && echo PRESENT || echo absent
absent

<prefix>_STARpass1/SJ.out.tab lands as expected, top-level SJ.pass1.out.tab is gone. Log.out and Log.progress.out are correctly absent — those stub writers were pulled out of this PR's scope (the placeholder content would have misled consumers; real STAR-parity for those files is left as a follow-up tracked on issue #28).

LGTM on the scoped-down PR.