Remove the deprecated CLI spellings after 2026-12-31

[jspaezp]

DEPRECATION_REMOVAL_DATE in rust/timsseek_cli/src/cli.rs is 2026-12-31. In the first release after that date, remove:

• the search subcommand (Command::Search), deprecated in favour of a bare invocation
• the --dotd-files alias of --raw-inputs
• the --speclib-file alias of --speclib-uri
• the --output-dir alias of --output-uri

Removing an alias also removes its DEPRECATED_FLAGS entry. every_deprecated_flag_is_a_clap_alias fails if the table keeps an entry whose alias is gone, and every_clap_alias_is_a_deprecated_flag fails if an alias survives with no entry, so the two cannot drift apart during the removal.

DEPRECATION_REMOVAL_DATE, DEPRECATED_SUBCOMMANDS, DEPRECATED_FLAGS, warn_deprecated_spellings, deprecation_warnings and replacement_advice all go with them, along with the warn_deprecated_spellings call in run() and the tests in cli.rs's mod tests that cover the deprecated spellings. run_inputs.rs has a test asserting the aliases resolve exactly as the canonical spellings do; that one goes too.

Filed so the date is scheduled work rather than a constant nobody reads.