CLI: remaining gaps after the PROJECT read fixes (#5845, #5942, #6030)

Summary

The recent fixes stopped version, help and completion from failing on a bad PROJECT file. A few cases are still wrong on master (506e94a). One of them deletes user files.

1. alpha generate --plugins deletes the project on an unknown layout

The layout names a plugin the CLI does not have. --plugins does not make that project usable, but alpha generate still wipes the directory before it fails:

$ cat PROJECT
version: "3"
layout:
- gone.example.com/v1
$ ls
PROJECT  notes.txt
$ kubebuilder alpha generate --plugins go.kubebuilder.io/v4
ERROR CLI run failed error=error executing command: no plugin could be resolved with key "gone.example.com/v1"
$ echo $?
1
$ ls -A
$

Expected: it fails and leaves every file in place.

2. A bad --plugins value on a command group is ignored

$ kubebuilder create --plugins //
Scaffold a Kubernetes API or webhook.
...
$ echo $?
0

Expected: the bad value is reported and the exit code is 1, as it is for kubebuilder create api --plugins //. Same for kubebuilder alpha --plugins //.

3. TAB no longer offers the flags of the plugins in layout

With a layout that names deploy-image.go.kubebuilder.io/v1-alpha:

$ kubebuilder create api --i<TAB>

Expected: --image, --image-container-command, --image-container-port. Now nothing is offered.

4. Commands added by other tools (WithExtraCommands, WithExtraAlphaCommands)

For projects that build their own CLI on pkg/cli, such as Operator-SDK:

• On a broken PROJECT file, the command is refused, but the tool's Args check has already run. It should not run.
• tool docs --plugins --help shows help, but runs the tool's Args check first.
• With no PROJECT file, a Run, PreRun or PersistentPreRun the tool sets after handing the command over does not run.

5. The first-word rule uses the command name, not the word typed

A tool command named docs with the alias version:

• tool docs runs on a broken PROJECT file. It should be refused.
• A command named docs typed as tool version is refused. It should run, because version is the first word.

6. A second run can scaffold with the wrong plugin chain

A tool builds the command tree for one plugin chain, then runs create api in a project whose layout names another. The first run fails, as it should. A second run on the same CLI scaffolds with the chain the tree was built from. It should fail again.

How this was found

Black-box tests that build master and run the CLI, plus small programs that use pkg/cli as a library.