filter: Remove deprecated `--output` and `-o` options

Context: https://github.com/nextstrain/augur/blob/d77c2753a6afcf7b7e2191046c0444def6646256/DEPRECATED.md#L7-L12 Before removing, we should consider updating internal usage. Results from [code search](https://github.com/search?q=org%3Anextstrain+NOT+is%3Aarchived+%2Faugur+filter%5Cb%28%3F%3A%5B%5Cs%5C%5C%5D%2B-%5CS%2B%5B%5Cs%5C%5C%5D%2B%5CS%2B%29*%5B%5Cs%5C%5C%5D%2B--sequences%5B%5Cs%5C%5C%5D%2B%5B%5E%5Cs%5C%5C%5D%2B%28%3F%3A%5B%5Cs%5C%5C%5D%2B-%5CS%2B%5B%5Cs%5C%5C%5D%2B%5CS%2B%29*%5B%5Cs%5C%5C%5D%2B%28%3F%3A--output%7C-o%29%5B%5Cs%5C%5C%5D%2B%5B%5E%5Cs%5C%5C%5D%2B%2F&type=code): - [ ] augur - [docs/usage/augur_snakemake.md](https://github.com/nextstrain/augur/blob/d77c2753a6afcf7b7e2191046c0444def6646256/docs/usage/augur_snakemake.md?plain=1#L21) - [ ] augur - [docs/usage/cli/index.rst](https://github.com/nextstrain/augur/blob/d77c2753a6afcf7b7e2191046c0444def6646256/docs/usage/cli/index.rst#L43) - [ ] avian-flu - [quickstart-build/Snakefile](https://github.com/nextstrain/avian-flu/blob/dadbde0e0d0f3d0540b9686d95c80cd9b03122e8/quickstart-build/Snakefile#L136) - [ ] docs.nextstrain.org - [src/tutorials/creating-a-phylogenetic-workflow-with-VCF-input.rst](https://github.com/nextstrain/docs.nextstrain.org/blob/46f24b446e73643fe746c041a5b2b05d58e6ad78/src/tutorials/creating-a-phylogenetic-workflow-with-VCF-input.rst#L82) - [ ] docs.nextstrain.org - [src/tutorials/creating-a-phylogenetic-workflow.rst](https://github.com/nextstrain/docs.nextstrain.org/blob/46f24b446e73643fe746c041a5b2b05d58e6ad78/src/tutorials/creating-a-phylogenetic-workflow.rst#L139) - [ ] enterovirus_d68 - [Snakefile](https://github.com/nextstrain/enterovirus_d68/blob/b135b964ca7928556d4c193a5891c6e454296565/Snakefile#L641) - [ ] hmpv - [nextclade/rules/prepare_sequences.smk](https://github.com/nextstrain/hmpv/blob/69bd4176fc2246136d629220cf7f2226b3f42af6/nextclade/rules/prepare_sequences.smk#L48) - [ ] lassa - [phylogenetic/rules/prepare_sequences.smk](https://github.com/nextstrain/lassa/blob/ba067af24d721138907ba8623c74c344b60534ad/phylogenetic/rules/prepare_sequences.smk#L177) - [ ] measles - [nextclade_genome/Snakefile](https://github.com/nextstrain/measles/blob/e1635b4ada20f8683ca67075deef5a06919803a9/nextclade_genome/Snakefile#L55) - [ ] measles - [nextclade/rules/prepare_sequences.smk](https://github.com/nextstrain/measles/blob/e1635b4ada20f8683ca67075deef5a06919803a9/nextclade/rules/prepare_sequences.smk#L72) - [ ] mers - [Snakefile](https://github.com/nextstrain/mers/blob/f2220554ec55883dc84e366367d52a3a420144b5/Snakefile#L73) - [ ] rabies - [phylogenetic/rules/prepare_sequences.smk](https://github.com/nextstrain/rabies/blob/2e6c55c9555e6dabdd5f8f19e2c202417f778085/phylogenetic/rules/prepare_sequences.smk#L60) - [ ] rsv - [nextclade/Snakefile](https://github.com/nextstrain/rsv/blob/fc6c095c3983d9f53eafdb3b68cace7d76d517e4/nextclade/Snakefile#L403) - [ ] rsv - [workflow/snakemake_rules/core.smk](https://github.com/nextstrain/rsv/blob/fc6c095c3983d9f53eafdb3b68cace7d76d517e4/workflow/snakemake_rules/core.smk#L75) - [ ] spheres-augur-build - [workflow/snakemake_rules/main_workflow.smk](https://github.com/nextstrain/spheres-augur-build/blob/18abd1846769a0db6e596812c479cf5b3603b656/workflow/snakemake_rules/main_workflow.smk#L38) - [ ] tb - [Snakefile](https://github.com/nextstrain/tb/blob/e00f457342645ac2d9698922d9a9c4cda4bdc4bc/Snakefile#L446) - [ ] vcf-input-tutorial - [Snakefile](https://github.com/nextstrain/vcf-input-tutorial/blob/69c2bd46e1589b07a1fa6c37c09db5043d2ed609/Snakefile#L30) - [ ] zika - [phylogenetic/rules/prepare_sequences.smk](https://github.com/nextstrain/zika/blob/d72cdcc0d31b46253c0b864948ecf0d1db64d015/phylogenetic/rules/prepare_sequences.smk#L52) - [ ] zika-tutorial - [Snakefile](https://github.com/nextstrain/zika-tutorial/blob/1c7f5936b03be478463174c60f166cb8e4426d70/Snakefile#L52)