Command line flags not overriding configuration file values

[spiffcs]

What happened:
When running syft -vv alpine:latest an error will occur if the configuration file is also set for verbosity.

What you expected to happen:
No error for syft to occur with command line flags and config set.

How to reproduce it (as minimally and precisely as possible):

run syft -vv alpine:latest with a configuration file also configured with log settings

log:
  # use structured logging
  # same as SYFT_LOG_STRUCTURED env var
  structured: false

  # the log level; note: detailed logging suppress the ETUI
  # same as SYFT_LOG_LEVEL env var
  level: "error"

  # location to write the log file (default is not to have a log file)
  # same as SYFT_LOG_FILE env var
  file: ""

Anything else we need to know?:
Community Meeting origin 8/4

Environment:

• Output of syft version: v0.53.4
• OS (e.g: cat /etc/os-release or similar):
• OSX

[kzantow]

NOTE: this looks like the command line precedence has an issue. It was just reported the same thing was happening for --output on the community Slack: https://anchorecommunity.slack.com/archives/C4PJFNEEM/p1667844831946429

[kzantow]

There is also a problem with command line flags overriding any config. An example is:

SYFT_OUTPUT=table syft alpine:latest -o json

... outputs the table instead of json but the command line parameter should override the environment variable (and config file).