pwm: the logo by default, output folders as input, a file picker; saves never overwrite (0.16.7)

[YPARK]

What changes

• The logo by default. faba pwm shows the sequence logo full screen unless --batch-process (alias --batch-mode) is given, or there is no terminal. -I/--interactive is gone from pwm, pileup and metagene: the view is the default, so --batch-process is the only switch. Old command lines with -I now fail to parse.
• Output folders as input. faba pwm out/ reads the folder's site table of --modality (m6A, else A-to-I) against its recorded genome; a run record in it works too.
• A picker when no sites are given. The same browser as pileup and metagene: mark site tables, or choose a faba folder.
• Several site tables. They are read in parallel and pooled into one set of sites. With --source reference they must record the same genome, or --genome names one; this is checked before any reading.
• A genome when none is recorded. In the view, with no -f and no recorded genome found on this machine, a picker lists FASTA files; Tab downloads one from GENCODE or Ensembl into ~/faba_refs/, as faba run does, starting on the source whose chromosome names match the sites. --batch-process still stops with the error.
• Parallel reference reads. --source reference reads the FASTA across threads, a reader per chunk of sites (same output, byte for byte, on the chr19 test set).
• APA sites keep their strand. apa_components.parquet gains a strand column (the UTR's), and the site reader uses it, so pwm reverse-complements minus-strand APA sites as it does m6A and A-to-I ones. Tables written before have none: read as forward, with a warning to rerun faba apa.
• BAMs stay positional. .bam, .cram and .sam arguments are reads, the rest sites, so faba pwm -s sites.parquet sample.bam --source reads works as before. BAMs given without --source reads are named in a warning.
• -o is optional. With --batch-process and no -o, the PWM goes to {sites}.pwm.tsv in the current folder; in the view it is written only when -o is given.
• A BAM read error is an error. It used to panic; under the new spinner that left the view spinning forever.

Saved figures never overwrite

The save prompt every figure view shares (pileup, metagene, pwm) now offers a name no save has used yet (pwm_logo, pwm_logo_2, …). Typing a name whose .pdf or .png exists keeps the prompt open with the next free one and says why.

The picker's key hints

They no longer get cut off: three lines (moving, marking, finishing), with the list sized to leave room for them.

One set of key rules

An audit of every view's keys, applied:

• Enter opens or chooses, never quits; Ctrl+R applies, starts, or submits any open line (save names, searches, typed values).
• Esc goes back one level (pileup's browser → its gene list; a top-level view quits); q quits; Ctrl-C asks first wherever q does (faba run setup, now on any change; qc with changed thresholds).
• Downloads: s stops, Esc hides, the folder is named first, and the pop-up lists its keys, in faba run and the reference picker alike.
• Same letter, same meaning: +/- finer/coarser in metagene as in pileup; m/M modality in pileup as in qc (mirror → v, previous site → N); pwm's bits/frequency → b; qc's annotation browser g → a (g is pileup's gene list).
• Asks before losing work: R (reset every flag); Space on a folder with files marked.
• Feedback: the busy spinner says it cannot stop halfway; Enter on a file in the input picker says Space marks.
• Footers never cut a key off: tui::wrap_help wraps them onto more lines at any width, keeping each key with its description; tests check every footer at 80 (60) columns.
• Documented as one paragraph in docs/profiling-methods.md §7.

Shared pieces

• crate::tui::batch: "batch, or no terminal" in one place, used by pileup, metagene and pwm. metagene now also writes its TSV when there is no terminal, instead of computing and dropping it.
• output_dir: site-table resolution, the default output name and the view title, shared by metagene and pwm.
• Reference downloads: the download pop-ups moved beside the download code (pipeline::tui::fetch), so faba run and pwm draw the same ones; the hint names whose chromosome names it matched (your BAMs, or your sites). is_fasta joins is_annotation in the shared browser.
• The spinner ends when its work dies, rather than spinning on.
• when_terminal is gone; its warning named the retired --interactive.

Checks

• cargo test: all pass but pipeline::tui::tests::a_folder_with_files_is_refused_as_the_output, which fails on main too.
• cargo clippy --all-targets -D warnings is clean, with and without --features hdf5.
• cargo fmt is applied.