refactor(cli): remove obsolete package layout

Author: jdalton

docs/cli-exe-migration.md

@@ -30,7 +30,7 @@ The split in one line: **doctor enforces time, optimize enforces shape.**
 
 ## The doctor command (new)
 
-`packages/cli/src/commands/doctor/` - first pass is deliberately small:
+`src/command/doctor/` - first pass is deliberately small:
 
 1. **Soak-time enforcement** (moved from the optimize draft):
    `ensurePnpmWorkspaceMinReleaseAge(repoRoot)` for pnpm repos - add at

docs/design/optimize-doctor-split.md

@@ -8,7 +8,7 @@ bazel mod show_extension @rules_jvm_external//:extensions.bzl%maven
 
 That command exits non-zero in two situations that mean opposite things. Telling
 them apart is the whole job of the classifier in
-`packages/cli/src/commands/manifest/bazel/bazel-repo-discovery.mts`, and getting
+`src/command/manifest/bazel/bazel-repo-discovery.mts`, and getting
 it wrong is a security problem rather than a cosmetic one.
 
 ## The two failures

docs/references/repo/bazel-extension-probe.md

@@ -3,7 +3,7 @@
 End-to-end tests run the real CLI, which means they run code that wants to
 write to a home directory: config files, package-manager caches, credential
 stores. Left alone, a test run would scribble on the machine it runs on. The
-helpers in `packages/cli/test/helpers/cli-execution.mts` prevent that by
+helpers in `test/helpers/cli-execution.mts` prevent that by
 pointing every such variable at a throwaway directory.
 
 There are two helpers because there are two ways a test reaches the CLI, and