fix(uninstall): remove the CLI binaries too, not just agent configs (#1254)

* fix(uninstall): remove the CLI binaries too, not just agent configs (#1071)

`codegraph uninstall` swept agent configurations and stopped — every
installed binary stayed behind, so `codegraph` still ran afterward. Three
disconnected paths each removed a fraction of an installation (uninstall:
configs; install.sh --uninstall: the bundle; npm preuninstall: configs +
npm's own package), and none cleared a shadowed second install — the
uninstall edition of the #1071 PATH shadow.

The uninstall now PLANS every install present on the machine — the bundle
layout(s) (running binary's own, the platform default, a custom
CODEGRAPH_INSTALL_DIR), the npm global package (found by asking
`npm root -g`, so nvm/fnm/volta prefixes resolve correctly), and the
bin-dir launcher link (only when it verifiably points into a detected
install) — confirms with the user, then removes them all. `--yes` skips
the prompt; the new `--keep-cli` flag keeps the old configs-only behavior.

Safety rules: a source checkout is reported, never deleted; a
project-local npm install is left to the project; on unix the default
install dir doubles as the machine state dir, so only the install
artifacts (versions/, current) are removed there — telemetry choice and
daemon records survive. Windows can't delete a running exe but can rename
it (the in-place upgrade's trick): a locked node.exe is renamed aside and
surfaced as a one-file leftover instead of failing the removal, and npm
is routed through cmd.exe (a direct .cmd spawn EINVALs on modern Node).

Planner/executor are split with injected side effects (the upgrade
orchestrator's convention) and unit-tested across the shadow case,
state-dir preservation, custom dirs, foreign-shim protection, and the
locked-exe dance; validated end-to-end on macOS against a fake HOME.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(uninstall): key path math on the target platform, not the host

Real-Windows validation caught it: the planner/executor used the host
path module, so win32 fixtures were meaningless on a POSIX host and
POSIX fixtures failed on the Windows VM. Same convention as
detectInstallMethod now — path.win32/path.posix chosen by the injected
platform.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(upgrade): route npm through cmd.exe on Windows — a direct npm.cmd spawn EINVALs on modern Node

Found while validating the uninstall change on the Windows VM: upgradeNpm
spawned npm.cmd without a shell, which every current Node rejects with
EINVAL (the CVE-2024-27980 hardening) — so `codegraph upgrade` on a
Windows npm install failed before doing anything. Verified live on the VM:
spawnSync('npm.cmd') → EINVAL; cmd.exe /d /s /c npm → works.

npmInvocation moves into the upgrade orchestrator (remove-binary imports
it from there — same direction as its existing imports, no cycle), and the
win32 test now pins the WORKING invocation instead of the broken one.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

README.md

@@ -122,12 +122,14 @@ Auto-sync is enabled by default. CodeGraph watches the project and updates the g
 
 ### Uninstall
 
-Changed your mind? One command removes CodeGraph from every agent it configured:
+Changed your mind? One command removes CodeGraph from every agent it configured **and** the CLI itself — every install it finds (standalone bundle, npm global package, launcher link), shown to you before anything is deleted:
 
 ```bash
 codegraph uninstall
 ```
 
+Pass `--keep-cli` to remove only the agent configurations and keep the CLI installed.
+
 <sub>Reverses the installer — strips CodeGraph's MCP server config, instructions, and permissions from each configured agent. Your project indexes (`.codegraph/`) are left untouched; remove those per-project with `codegraph uninit`. Use `--target` to remove from specific agents, or `--yes` to run non-interactively.</sub>
 
 ---
@@ -540,7 +542,7 @@ The exact text is `src/mcp/server-instructions.ts` — the single source of trut
 ```bash
 codegraph                         # Run interactive installer
 codegraph install                 # Run installer (explicit)
-codegraph uninstall               # Remove CodeGraph from your agents (inverse of install)
+codegraph uninstall               # Remove CodeGraph from your agents AND the CLI (--keep-cli for configs only)
 codegraph init [path]             # Initialize a project + build its graph (one step)
 codegraph uninit [path]           # Remove CodeGraph from a project (--force to skip prompt)
 codegraph index [path]            # Full index (--force to re-index, --quiet for less output)