fix(cli): print each error once

[thanhleviet]

Every error from atb reached the user twice.

$ atb query --runs ERR9999999999 --columns sample_accession
Warning: 1 of 1 run accession(s) are not in run.parquet: ERR9999999999
Error: none of the 1 run accession(s) are in run.parquet
none of the 1 run accession(s) are in run.parquet

internal/cli/root.go set SilenceUsage but not SilenceErrors, so cobra
printed the Error: ... line when the command returned, and cmd/atb/main.go
printed the same message again. One failure looked like two. It affected every
error path, not one command.

The fix

Silence cobra's reporting and leave main as the only printer.

The alternative - dropping main's print and letting cobra report - puts the
error before WaitForUpdateCheck() runs, and that check also writes to
stderr, so a failure could end up buried above the update banner. Printing from
main keeps the error as the last line. It keeps the Error: prefix, which
matters because atb writes progress and warnings to stderr too; without a
prefix a bare error line is indistinguishable from Resolved 99 run accession(s)....

run() is extracted from main() so the exit path is testable. Behavior of
main is otherwise unchanged.

After

$ atb query --runs ERR9999999999 --columns sample_accession
Warning: 1 of 1 run accession(s) are not in run.parquet: ERR9999999999
Error: none of the 1 run accession(s) are in run.parquet

Verification

• 3 new tests in cmd/atb/main_test.go, written first and watched fail
  (error reported 2 time(s), want 1). cmd/atb was previously untested, so
  the suite goes from 21 to 22 covered packages.
• Checked on a real binary across four error paths - unknown column, unresolved
  run accession, unknown flag, unknown command - each prints once and exits 1.
  Unknown-command takes a different cobra branch, so it is covered separately.
• Success paths are byte-identical to released v0.21.0 on both stdout and
  stderr; only error output changed.
• go vet clean, gofmt clean on the touched files, make docs produces no
  diff.