Fixes from internal

[bufdev]

• Fixes issue where Zsh completion would fail due to some flags having brackets in their description. This is done via upgrading spf13/cobra to master for now via Square brackets in the description causes problems with zsh spf13/cobra#1129. Fixes Zsh/Fish completion failing #105.
• Fixes issue where non-builtin protoc plugin invocations would not have errors properly propagated.
• Fixes issue where multiple --.*_opt flags, --.*_opt flags with commas, or --.*_out flags with options that contained commas, would not be properly added.
• Dogfoods protoc --by_dir flag.

[codecov]

Codecov Report

Merging #110 into master will decrease coverage by 0.05%.
The diff coverage is 55.81%.

@@            Coverage Diff             @@
##           master     #110      +/-   ##
==========================================
- Coverage   73.04%   72.98%   -0.06%     
==========================================
  Files         179      179              
  Lines       10647    10668      +21     
==========================================
+ Hits         7777     7786       +9     
- Misses       2114     2123       +9     
- Partials      756      759       +3     

Impacted Files	Coverage Δ
internal/buf/cmd/buf/buf.go	0.00% <ø> (ø)
internal/buf/cmd/buf/internal/protoc/errors.go	8.16% <0.00%> (+4.08%)	⬆️
internal/pkg/app/appproto/appproto.go	53.84% <ø> (ø)
...al/pkg/app/appproto/appprotoexec/binary_handler.go	67.39% <0.00%> (-4.71%)	⬇️
internal/pkg/app/appproto/response_writer.go	65.11% <35.71%> (-14.89%)	⬇️
internal/buf/cmd/buf/internal/protoc/flags.go	80.28% <78.26%> (+1.81%)	⬆️
internal/buf/cmd/buf/internal/protoc/plugin.go	52.85% <100.00%> (ø)
internal/buf/bufanalysis/bufanalysis.go	66.31% <0.00%> (-2.11%)	⬇️
internal/buf/bufcheck/internal/config.go	74.69% <0.00%> (-1.21%)	⬇️
internal/pkg/fetch/ref_parser.go	92.89% <0.00%> (-0.95%)	⬇️
... and 2 more

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