Add --skip/--skip-only flags; make group skip trim its dependency subtree

docs/docs/commands/doctor.md

@@ -23,6 +23,17 @@ Commands:
 
 `scope doctor run` is used to execute all the doctor steps. All checks will be run, if you want to only run specific checks, the `--only` flag with the name of the check to run. This option can be provided multiple times.
 
+If you want to remove a group from the run instead, use `--skip`. Skipping a group also removes any
+of its dependencies that aren't also required by another group still in the run — a dependency
+shared with a non-skipped group keeps running. This option can be provided multiple times.
+
+If you only want to remove the named group itself, and let its dependencies keep running, use
+`--skip-only` instead.
+
+A group can also skip itself via its [`skip` config](../models/ScopeDoctorGroup.mdx#skip)
+(`skip: true` or a `skip` command); it's resolved the same way `--skip` is, trimming that group's
+dependency subtree.
+
 By default, any provided fix's will be run. If you don't want to run fixes add `--fix=false` to disable fixing issues.
 
 When using a [ScopeDoctorGroup](../models/ScopeDoctorGroup.mdx), the checksum of files are stored on disk. If you need to disable caching, add `--no-cache`.
@@ -34,6 +45,8 @@ Usage: scope doctor run [OPTIONS]
 
 Options:
   -o, --only <ONLY>                  When set, only the checks listed will run
+      --skip <SKIP>                  When set, these groups are removed from the run, along with any dependency that isn't also required by a group that's still included
+      --skip-only <SKIP_ONLY>        When set, only the named groups are removed from the run; their dependencies still run
   -f, --fix <FIX>                    When set, if a fix is specified it will also run [default: true] [possible values: true, false]
   -n, --no-cache                     When set cache will be disabled, forcing all file based checks to run
       --yolo                         Automatically approve all fix prompts without asking

docs/docs/models/ScopeDoctorGroup.mdx

@@ -73,6 +73,17 @@ In the event there are no defined check, the fix will _always_ run.
 When the checks determine that something isn't correct, a fix is the way to automate the resolution.
 When provided, `scope` will run them in order.
 
+## Skip
+
+`spec.skip` lets a group opt itself out of a run, either unconditionally (`skip: true`) or based
+on a command's exit code (`skip: { command: ... }`, skipped when the command exits `0`).
+
+The skip decision is resolved during planning, before the run graph is built, so it behaves the
+same as passing `--skip <name>` on the command line: the group is removed along with any
+dependency that isn't also required by another group still in the run. A shared dependency (one
+also required by a non-skipped group) is kept. The skipped group is still reported in the run
+summary; its dependencies that get trimmed along with it are not.
+
 ## Commands
 
 A command can either be relative, or use the PATH.

src/doctor/commands/list.rs

@@ -4,7 +4,7 @@ use anyhow::Result;
 use clap::Args;
 use tracing::instrument;
 
-use crate::doctor::runner::compute_group_order;
+use crate::doctor::runner::{GroupOrderParams, compute_group_order};
 use crate::report_stdout;
 use crate::shared::prelude::{DoctorGroup, FoundConfig};
 use crate::shared::print_details;
@@ -28,7 +28,12 @@ pub fn generate_doctor_list(found_config: &FoundConfig) -> Vec<DoctorGroup> {
             .filter(|(_, v)| v.run_by_default)
             .map(|(k, _)| k.to_string()),
     );
-    let group_order = compute_group_order(&found_config.doctor_group, all_keys);
+    let group_order = compute_group_order(GroupOrderParams {
+        groups: &found_config.doctor_group,
+        desired_groups: &all_keys,
+        skip_subtree: &BTreeSet::new(),
+        skip_only: &BTreeSet::new(),
+    });
 
     group_order
         .iter()