Remove global flags from filesystem command (#772)

* Remove global flags from subcommands

If the global flags are added to the subcommand as well as being used
globally, their value will be overwritten when the arguments for the
subcommand are parsed. This leads to the value passed to the flag at the
global position being lost.

* Update readme

internal/app.go

@@ -386,13 +386,10 @@ func NewFilesystemCommand() *cli.Command {
 			&exitCodeFlag,
 			&skipUpdateFlag,
 			&clearCacheFlag,
-			&quietFlag,
 			&ignoreUnfixedFlag,
-			&debugFlag,
 			&removedPkgsFlag,
 			&vulnTypeFlag,
 			&ignoreFileFlag,
-			&cacheDirFlag,
 			&cacheBackendFlag,
 			&timeoutFlag,
 			&noProgressFlag,
@@ -421,13 +418,10 @@ func NewRepositoryCommand() *cli.Command {
 			&exitCodeFlag,
 			&skipUpdateFlag,
 			&clearCacheFlag,
-			&quietFlag,
 			&ignoreUnfixedFlag,
-			&debugFlag,
 			&removedPkgsFlag,
 			&vulnTypeFlag,
 			&ignoreFileFlag,
-			&cacheDirFlag,
 			&cacheBackendFlag,
 			&timeoutFlag,
 			&noProgressFlag,
@@ -455,13 +449,10 @@ func NewClientCommand() *cli.Command {
 			&outputFlag,
 			&exitCodeFlag,
 			&clearCacheFlag,
-			&quietFlag,
 			&ignoreUnfixedFlag,
-			&debugFlag,
 			&removedPkgsFlag,
 			&vulnTypeFlag,
 			&ignoreFileFlag,
-			&cacheDirFlag,
 			&timeoutFlag,
 			&ignorePolicy,
 
@@ -494,9 +485,6 @@ func NewServerCommand() *cli.Command {
 			&skipUpdateFlag,
 			&downloadDBOnlyFlag,
 			&resetFlag,
-			&quietFlag,
-			&debugFlag,
-			&cacheDirFlag,
 			&cacheBackendFlag,
 
 			// original flags