diff --git a/.changeset/fierce-quails-wave.md b/.changeset/fierce-quails-wave.md
new file mode 100644
index 000000000..6d3cec582
--- /dev/null
+++ b/.changeset/fierce-quails-wave.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 1442
+---
+**Antigravity config-dir resolution no longer shadows the active runtime** — when more than one of `~/.gemini/antigravity`, `antigravity-ide`, or `antigravity-cli` exists, GSD now resolves to the directory it actually installed into (marked by `gsd-core/VERSION`) instead of whichever directory existed first. Fixes silent misresolution where a CLI user who also had the Antigravity-IDE dir present was sent to the legacy dir (regression from #217).
diff --git a/CONTEXT.md b/CONTEXT.md
index 8c8f7127a..66409c256 100644
--- a/CONTEXT.md
+++ b/CONTEXT.md
@@ -119,7 +119,7 @@ Module owning runtime identity normalization at runtime-selection seams. Canonic
 Module owning validation for Installer Migration Module records and planned actions. It enforces migration metadata, explicit install scopes, ownership evidence for destructive/config actions, and runtime contract citations for runtime config rewrites before a migration can enter planning or apply.
 
 ### Installer Module
-Primary installer for all runtimes. Single production file: `bin/install.js` (generated). Exports: `install(isGlobal, runtime[, configDir])` → typed result `{ runtime, configDir, settingsPath, settings, statuslineCommand, updateBannerCommand }`; `uninstall(isGlobal, runtime[, configDir])`; `installRuntimeArtifacts(runtime, configDir, scope, resolvedProfile)`; `uninstallRuntimeArtifacts(runtime, configDir, scope)`; `writeManifest(configDir, runtime)`. Runtime enum: `allRuntimes` (15 values: claude, antigravity, augment, cline, codebuddy, codex, copilot, cursor, gemini, hermes, kilo, opencode, qwen, trae, windsurf). Directory helpers: `getDirName(runtime)` → local dir name; `getConfigDirFromHome(runtime, isGlobal)` → shell-quoted path fragment. Per-runtime global config-dir resolution is delegated to `gsd-core/bin/lib/runtime-homes.cjs:getGlobalConfigDir(runtime[, explicitDir])` — the canonical, env-var–aware projection (`explicitDir` override + opencode/kilo `*_CONFIG` file-path precedence); the legacy in-installer `getGlobalDir`/`getOpencodeGlobalDir`/`getKiloGlobalDir` were retired into it (#56). Runtime-specific helpers: `resolveKiloConfigPath(configDir)`, `configureKiloPermissions(isGlobal[, explicitDir])`. Claude-specific permission helpers: `mergeClaudePermissions(settings)` — non-destructively appends GSD-owned allow/deny entries (see `GSD_CLAUDE_ALLOW_PERMISSIONS`, `GSD_CLAUDE_DENY_PERMISSIONS` constants) to a Claude Code settings object; called from `finishInstall` for `runtime === 'claude'` only; uninstall removes exactly these entries (#768). Layout-driven artifact copy/removal delegates to `gsd-core/bin/lib/runtime-artifact-layout.cjs:resolveRuntimeArtifactLayout` (throws `TypeError` for unknown runtimes). Seven runtimes with non-recursive skill loaders (claude global, cline, qwen, hermes, augment, trae, antigravity) use a nested router layout: 6 `gsd-ns-*` router bundles emitted as top-level skills, with concrete skills nested at `<router>/skills/<name>/SKILL.md` (hermes prefix='': `skills/gsd/ns-*/…`). The remaining skills-runtimes (cursor, codex, copilot, windsurf, codebuddy, opencode, kilo) use the flat `skills/gsd-<stem>/` layout unchanged. See Skill Surface Budget Module and Runtime Artifact Layout Module.
+Primary installer for all runtimes. Single production file: `bin/install.js` (generated). Exports: `install(isGlobal, runtime[, configDir])` → typed result `{ runtime, configDir, settingsPath, settings, statuslineCommand, updateBannerCommand }`; `uninstall(isGlobal, runtime[, configDir])`; `installRuntimeArtifacts(runtime, configDir, scope, resolvedProfile)`; `uninstallRuntimeArtifacts(runtime, configDir, scope)`; `writeManifest(configDir, runtime)`. Runtime enum: `allRuntimes` (15 values: claude, antigravity, augment, cline, codebuddy, codex, copilot, cursor, gemini, hermes, kilo, opencode, qwen, trae, windsurf). Directory helpers: `getDirName(runtime)` → local dir name; `getConfigDirFromHome(runtime, isGlobal)` → shell-quoted path fragment. Per-runtime global config-dir resolution is delegated to `gsd-core/bin/lib/runtime-homes.cjs:getGlobalConfigDir(runtime[, explicitDir])` — the canonical, env-var–aware projection (`explicitDir` override + opencode/kilo `*_CONFIG` file-path precedence); the legacy in-installer `getGlobalDir`/`getOpencodeGlobalDir`/`getKiloGlobalDir` were retired into it (#56). The same module exposes `detectAntigravityDirAmbiguity(opts)` — a side-effect-free probe reporting whether multiple `~/.gemini/antigravity{,-ide,-cli}` dirs coexist and which one GSD's `gsd-core/VERSION` marker (the `dot-home-nested` `probeExists`) resolves to, for installer / `/gsd-update` operator guidance when a pre-#217 install landed in the wrong sibling dir (#1441). Runtime-specific helpers: `resolveKiloConfigPath(configDir)`, `configureKiloPermissions(isGlobal[, explicitDir])`. Claude-specific permission helpers: `mergeClaudePermissions(settings)` — non-destructively appends GSD-owned allow/deny entries (see `GSD_CLAUDE_ALLOW_PERMISSIONS`, `GSD_CLAUDE_DENY_PERMISSIONS` constants) to a Claude Code settings object; called from `finishInstall` for `runtime === 'claude'` only; uninstall removes exactly these entries (#768). Layout-driven artifact copy/removal delegates to `gsd-core/bin/lib/runtime-artifact-layout.cjs:resolveRuntimeArtifactLayout` (throws `TypeError` for unknown runtimes). Seven runtimes with non-recursive skill loaders (claude global, cline, qwen, hermes, augment, trae, antigravity) use a nested router layout: 6 `gsd-ns-*` router bundles emitted as top-level skills, with concrete skills nested at `<router>/skills/<name>/SKILL.md` (hermes prefix='': `skills/gsd/ns-*/…`). The remaining skills-runtimes (cursor, codex, copilot, windsurf, codebuddy, opencode, kilo) use the flat `skills/gsd-<stem>/` layout unchanged. See Skill Surface Budget Module and Runtime Artifact Layout Module.
 
 ### I/O Module
 Module owning the tool's CLI I/O primitives: `output()` result emission (with large-payload temp-file spillover via `GSD_TEMP_DIR`/`ensureGsdTempDir`/`reapStaleTempFiles`), `error()` stderr emission with exit-code mapping, and the JSON-error-mode toggle (`setJsonErrorMode`/`getJsonErrorMode`, `ERROR_REASON`). Extracted from the Core module per ADR-857 rollout phase 1 (#859) so feature modules (`graphify`, `intel`, `audit`, `profile-pipeline`) depend on a small I/O seam instead of the core god-module; the `core.cjs` re-export spine was retired in epic #1267, so callers import this leaf directly. Source of truth: `gsd-core/bin/lib/io.cjs` (generated from `src/io.cts`).
diff --git a/capabilities/antigravity/capability.json b/capabilities/antigravity/capability.json
index dad076a55..a6065c3b4 100644
--- a/capabilities/antigravity/capability.json
+++ b/capabilities/antigravity/capability.json
@@ -21,7 +21,8 @@
         "antigravity",
         "antigravity-ide",
         "antigravity-cli"
-      ]
+      ],
+      "probeExists": "gsd-core/VERSION"
     },
     "configFormat": "settings-json",
     "artifactLayout": {
diff --git a/docs/adr/1016-runtime-capability-descriptor.md b/docs/adr/1016-runtime-capability-descriptor.md
index 1b882fac9..6fe0b3bef 100644
--- a/docs/adr/1016-runtime-capability-descriptor.md
+++ b/docs/adr/1016-runtime-capability-descriptor.md
@@ -34,7 +34,7 @@ configHome: {
   parent?: string,              // for dot-home-nested: e.g. '.gemini' (antigravity), '.codeium' (windsurf)
   env: string[],                // ordered override env vars, e.g. ['CLAUDE_CONFIG_DIR'] (required; may be empty)
   probe?: string[],             // ordered candidate subpaths; first existing wins (antigravity, kimi)
-  probeExists?: string,         // if set, select the first probe candidate where <candidate>/<probeExists> exists (kimi: 'skills')
+  probeExists?: string,         // marker sub-path on a probe candidate. generic-agents-root: hard filter (kimi: 'skills'). dot-home-nested: marker-priority preference, then bare-existence fallback (antigravity: 'gsd-core/VERSION', #213/#217) — see amendment below
   skillsHome?: { kind, name, ... }  // override when the skills dir ≠ config dir (kilo only)
 }
 ```
@@ -48,6 +48,10 @@ This absorbs kilo (`skillsHome` split), kimi & antigravity (`probe`), windsurf (
 
 `configHome` resolution is **pure and read-only** (a first-existing probe; no `mkdirSync` — verified in `runtime-homes.cts`). Any directory creation at install time is the `configFormat` permissions-writer's responsibility (opencode/kilo), never the descriptor-resolution step — so `configHome` carries no `createIfMissing` flag.
 
+#### Amendment — `probeExists` on `dot-home-nested` (#1441, 2026-06-18)
+
+`probeExists` was originally honoured only by `generic-agents-root` (kimi), as a *hard filter*. It is now also honoured by `dot-home-nested`, where it acts as a *preference*: probing first returns the candidate whose `<candidate>/<probeExists>` exists (the dir GSD installed into, marked by `gsd-core/VERSION`), then falls back to the legacy first-bare-existing pass, then `probe[0]`. When `probeExists` is absent the behaviour is byte-identical to the original first-bare-existing probe, so other `dot-home-nested` runtimes (e.g. windsurf, which has no `probe`) are unaffected. This fixes silent misresolution where an active sibling dir (the Antigravity-IDE `~/.gemini/antigravity`) shadowed a CLI install in `~/.gemini/antigravity-cli` — a regression introduced by #217. The existing `probeExists` field name is reused rather than introducing a parallel `probeMarker`, keeping the `configHome` vocabulary closed.
+
 ### 2. `configFormat` — the existing closed enum (unchanged)
 
 `settings-json | toml | markdown | markdown-dir | none`. Cursor is `none` (it writes no settings file — its only managed file is the hooks manifest, captured by `hooksSurface`, not `configFormat`). opencode/kilo are `settings-json` with a JSONC **permissions sidecar** expressed by an optional `permissions: 'opencode-jsonc' | 'kilo-jsonc' | 'none'` sub-field (the only two runtimes that write one).
diff --git a/docs/reference/capability-manifest.md b/docs/reference/capability-manifest.md
index b5f4ee3fa..678bac000 100644
--- a/docs/reference/capability-manifest.md
+++ b/docs/reference/capability-manifest.md
@@ -138,7 +138,7 @@ Runtime capabilities describe how GSD projects its artefacts onto one host CLI.
 
 | Axis | Field | Type summary |
 |---|---|---|
-| Config home | `runtime.configHome` | Structured object with `kind` (`dot-home` \| `dot-home-nested` \| `xdg` \| `generic-agents-root`), `name`, optional `parent`, `env[]`, `probe[]`, `probeExists`, `skillsHome`. |
+| Config home | `runtime.configHome` | Structured object with `kind` (`dot-home` \| `dot-home-nested` \| `xdg` \| `generic-agents-root`), `name`, optional `parent`, `env[]`, `probe[]`, `probeExists`, `skillsHome`. `probeExists` is an optional sub-path applied to probe candidates: for `generic-agents-root` it is a hard filter (a candidate qualifies only if `<candidate>/<probeExists>` exists); for `dot-home-nested` it is a preference that makes probing pick the candidate GSD owns (e.g. `gsd-core/VERSION`) over a bare-existing sibling before falling back — see ADR-1016 and #213/#217. |
 | Config format | `runtime.configFormat` | Closed enum: `settings-json` \| `toml` \| `markdown` \| `markdown-dir` \| `none`. |
 | Artefact layout | `runtime.artifactLayout` | Object with `global` and `local` arrays of `ArtifactKind` (`kind`, `destSubpath`, `prefix`, `nesting`, `recursive`, `stage`). |
 | Command style | `runtime.commandStyle` | Closed enum: `slash-hyphen` \| `shell-var`. |
diff --git a/gsd-core/bin/lib/capability-registry.cjs b/gsd-core/bin/lib/capability-registry.cjs
index e7d79fd2c..dbc5e9157 100644
--- a/gsd-core/bin/lib/capability-registry.cjs
+++ b/gsd-core/bin/lib/capability-registry.cjs
@@ -83,7 +83,8 @@ const capabilities = {
           "antigravity",
           "antigravity-ide",
           "antigravity-cli"
-        ]
+        ],
+        "probeExists": "gsd-core/VERSION"
       },
       "configFormat": "settings-json",
       "artifactLayout": {
@@ -2740,7 +2741,8 @@ const runtimes = {
           "antigravity",
           "antigravity-ide",
           "antigravity-cli"
-        ]
+        ],
+        "probeExists": "gsd-core/VERSION"
       },
       "configFormat": "settings-json",
       "artifactLayout": {
diff --git a/src/runtime-homes.cts b/src/runtime-homes.cts
index 1d122e6a4..0b5e70e18 100644
--- a/src/runtime-homes.cts
+++ b/src/runtime-homes.cts
@@ -76,6 +76,20 @@ interface DotHomeNestedDescriptor {
   parent: string;
   env: string[];
   probe?: string[];
+  /**
+   * Optional sub-path that qualifies which probe candidate GSD actually owns
+   * (e.g. `gsd-core/VERSION`). The same field name and check used by the
+   * generic-agents-root descriptor — unified vocabulary per ADR-1016. The
+   * resolution *strength* differs per kind: generic-agents-root treats it as a
+   * hard filter (a candidate only qualifies if `<candidate>/<probeExists>`
+   * exists), whereas dot-home-nested treats it as a *preference* — probing runs
+   * in two passes: first the candidate whose `<candidate>/<probeExists>` exists
+   * wins (the dir GSD installed into), then a bare-existence pass, then
+   * `probe[0]`. Without it, behaviour is the legacy first-bare-existing-wins
+   * probe, so other dot-home-nested runtimes (e.g. windsurf, which has no probe)
+   * are unaffected. See ADR-1016 and #213/#217 (antigravity split).
+   */
+  probeExists?: string;
   skillsHome?: ConfigHomeDescriptor;
 }
 
@@ -163,7 +177,20 @@ export function resolveConfigHomeFromDescriptor(
       }
       const base = path.join(home, configHome.parent);
       if (configHome.probe && configHome.probe.length > 0) {
-        // probe each candidate under base; return first that exists
+        // Pass 1 (marker-priority): when probeExists is declared, prefer the
+        // candidate GSD actually owns (its `<candidate>/<probeExists>` exists).
+        // This disambiguates an active-but-shadowing sibling dir (e.g. the
+        // Antigravity-IDE `~/.gemini/antigravity` dir) from the dir GSD was
+        // installed into, instead of blindly taking the first dir that exists.
+        if (configHome.probeExists) {
+          for (const candidate of configHome.probe) {
+            const resolved = path.join(base, candidate);
+            if (existsSyncFn(path.join(resolved, configHome.probeExists))) {
+              return resolved;
+            }
+          }
+        }
+        // Pass 2 (legacy bare-existence): first candidate dir that exists.
         for (const candidate of configHome.probe) {
           const resolved = path.join(base, candidate);
           if (existsSyncFn(resolved)) return resolved;
@@ -239,11 +266,72 @@ export function resolveAntigravityGlobalDir(opts: ResolveAntigravityOpts = {}):
       parent: '.gemini',
       env: ['ANTIGRAVITY_CONFIG_DIR'],
       probe: ['antigravity', 'antigravity-ide', 'antigravity-cli'],
+      // Prefer the candidate GSD installed into (carries gsd-core/VERSION) over
+      // a bare-existing sibling. Without this, a CLI user (antigravity-cli) who
+      // also has the IDE's ~/.gemini/antigravity dir is shadowed to the legacy
+      // dir because it is probed first. See #213/#217. The posix-slash literal
+      // matches capabilities/antigravity/capability.json; both normalize via
+      // path.join at the check site, so Windows backslash handling is covered.
+      probeExists: 'gsd-core/VERSION',
     },
     { env, home, existsSync: existsSyncFn },
   );
 }
 
+export interface AntigravityAmbiguity {
+  /** True when more than one ~/.gemini/antigravity{,-ide,-cli} dir is present. */
+  ambiguous: boolean;
+  /** The dir GSD currently resolves to (where install/update will write). */
+  resolved: string;
+  /** All probe candidate dirs that exist on disk (absolute paths). */
+  presentDirs: string[];
+  /**
+   * Candidate dirs that carry the GSD marker (gsd-core/VERSION). When this has
+   * exactly one entry, resolution is unambiguous. Zero or >1 entries (or a
+   * marker in a dir other than the one a CLI/IDE user expects) is the #213/#217
+   * misinstall surface: a prior install may have landed in the wrong sibling dir.
+   */
+  gsdMarkedDirs: string[];
+  /** ANTIGRAVITY_CONFIG_DIR is the operator escape hatch; true when already set. */
+  envOverridden: boolean;
+}
+
+/**
+ * Detect whether the Antigravity config-dir resolution is ambiguous — i.e. more
+ * than one of ~/.gemini/{antigravity,antigravity-ide,antigravity-cli} exists, so
+ * a user upgrading from a pre-#217 install may have had GSD written into the
+ * wrong sibling dir (the legacy/IDE dir shadowing an active CLI dir).
+ *
+ * This is a pure, side-effect-free probe intended for the installer and
+ * /gsd-update to surface operator guidance (set ANTIGRAVITY_CONFIG_DIR or move
+ * gsd-core/ into the intended dir). The migration framework cannot relocate an
+ * install across sibling config dirs (it is bounded to a single configDir and
+ * has no cross-dir move primitive — see installer-migrations 004), so existing
+ * misinstalls are corrected by re-detection + operator guidance, not an
+ * automatic move.
+ */
+export function detectAntigravityDirAmbiguity(
+  opts: ResolveAntigravityOpts = {},
+): AntigravityAmbiguity {
+  const env: Record<string, string | undefined> = opts.env ?? process.env;
+  const home = opts.home ?? os.homedir();
+  const existsSyncFn = opts.existsSync ?? fs.existsSync;
+  const marker = path.join('gsd-core', 'VERSION');
+  const base = path.join(home, '.gemini');
+  const candidates = ['antigravity', 'antigravity-ide', 'antigravity-cli'].map((c) =>
+    path.join(base, c),
+  );
+  const presentDirs = candidates.filter((dir) => existsSyncFn(dir));
+  const gsdMarkedDirs = candidates.filter((dir) => existsSyncFn(path.join(dir, marker)));
+  return {
+    ambiguous: presentDirs.length > 1,
+    resolved: resolveAntigravityGlobalDir({ env, home, existsSync: existsSyncFn }),
+    presentDirs,
+    gsdMarkedDirs,
+    envOverridden: Boolean(env['ANTIGRAVITY_CONFIG_DIR']),
+  };
+}
+
 /**
  * Resolve Kimi's generic user root using Kimi CLI's documented first-existing
  * generic skills directory policy:
diff --git a/tests/install.test.cjs b/tests/install.test.cjs
index a2c84ad2c..f68b3e817 100644
--- a/tests/install.test.cjs
+++ b/tests/install.test.cjs
@@ -159,6 +159,46 @@ describe('getGlobalConfigDir/getConfigDirFromHome — antigravity 2.x layout det
       cleanup(home);
     }
   });
+
+  // #213/#217 coexistence regression (end-to-end through the registry descriptor).
+  // A CLI user who ALSO has the Antigravity-IDE's ~/.gemini/antigravity dir was
+  // previously shadowed to the legacy dir because it is probed first. The
+  // The probeExists marker (gsd-core/VERSION) makes the dir GSD installed into win.
+  test('coexistence: legacy antigravity + GSD-marked antigravity-cli both present → resolves to antigravity-cli', (t) => {
+    const home = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-antigravity-coexist-'));
+    t.after(() => cleanup(home));
+    // Both dirs exist on disk...
+    fs.mkdirSync(path.join(home, '.gemini', 'antigravity'), { recursive: true });
+    fs.mkdirSync(path.join(home, '.gemini', 'antigravity-cli', 'gsd-core'), { recursive: true });
+    // ...but only the cli dir carries the GSD marker.
+    fs.writeFileSync(path.join(home, '.gemini', 'antigravity-cli', 'gsd-core', 'VERSION'), '1.6.0\n');
+    process.env.HOME = home;
+    process.env.USERPROFILE = home;
+    assert.strictEqual(
+      getGlobalConfigDir('antigravity'),
+      path.join(home, '.gemini', 'antigravity-cli'),
+      'GSD-marked antigravity-cli must win over the bare-existing legacy antigravity dir',
+    );
+    assert.strictEqual(
+      getConfigDirFromHome('antigravity', true),
+      "'.gemini', 'antigravity-cli'",
+    );
+  });
+
+  test('coexistence: legacy antigravity carries the GSD marker (real 1.x install) → resolves to legacy even when cli dir exists bare', (t) => {
+    const home = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-antigravity-legacy-marked-'));
+    t.after(() => cleanup(home));
+    fs.mkdirSync(path.join(home, '.gemini', 'antigravity', 'gsd-core'), { recursive: true });
+    fs.writeFileSync(path.join(home, '.gemini', 'antigravity', 'gsd-core', 'VERSION'), '1.5.0\n');
+    fs.mkdirSync(path.join(home, '.gemini', 'antigravity-cli'), { recursive: true });
+    process.env.HOME = home;
+    process.env.USERPROFILE = home;
+    assert.strictEqual(
+      getGlobalConfigDir('antigravity'),
+      path.join(home, '.gemini', 'antigravity'),
+      'a genuine GSD install in the legacy dir must not be abandoned for a bare sibling',
+    );
+  });
 });
 
 describe('getGlobalConfigDir — explicit configDir overrides env for all runtimes', () => {
diff --git a/tests/runtime-homes-descriptor-drive.test.cjs b/tests/runtime-homes-descriptor-drive.test.cjs
index 9fd2a008a..074bd321a 100644
--- a/tests/runtime-homes-descriptor-drive.test.cjs
+++ b/tests/runtime-homes-descriptor-drive.test.cjs
@@ -29,6 +29,7 @@ const {
   resolveKimiGlobalDir,
   resolveConfigHomeFromDescriptor,
   resolveSkillsBaseFromDescriptor,
+  detectAntigravityDirAmbiguity,
 } = require(path.join(ROOT, 'gsd-core', 'bin', 'lib', 'runtime-homes.cjs'));
 
 const HOME = os.homedir();
@@ -393,6 +394,109 @@ describe('descriptor-driven equivalence: dot-home-nested antigravity probe hit/m
     }
   });
 
+  // ── #213/#217 coexistence regression: probeExists disambiguation ──────────
+  // Before probeExists on dot-home-nested, first-bare-existing-wins meant a CLI
+  // user (antigravity-cli) who also had the IDE's ~/.gemini/antigravity dir
+  // present was shadowed to the legacy dir (probed first). probeExists =
+  // 'gsd-core/VERSION' makes the dir GSD actually owns win, regardless of order.
+  const AG_PROBE = ['antigravity', 'antigravity-ide', 'antigravity-cli'];
+  const AG_MARKER = path.join('gsd-core', 'VERSION');
+
+  function antigravityDescriptor(withMarker) {
+    const d = {
+      kind: 'dot-home-nested',
+      name: 'antigravity',
+      parent: '.gemini',
+      env: ['ANTIGRAVITY_CONFIG_DIR'],
+      probe: AG_PROBE,
+    };
+    if (withMarker) d.probeExists = AG_MARKER;
+    return d;
+  }
+
+  test('coexistence: legacy antigravity + antigravity-cli both exist, only cli is GSD-marked → returns antigravity-cli', () => {
+    const home = '/home/u';
+    const cliDir = path.join(home, '.gemini', 'antigravity-cli');
+    const legacyDir = path.join(home, '.gemini', 'antigravity');
+    const markerPath = path.join(cliDir, AG_MARKER);
+    // Both dirs exist on disk; only the cli dir carries gsd-core/VERSION.
+    const existsSync = (p) =>
+      p === markerPath || p === cliDir || p === legacyDir;
+    const result = resolveConfigHomeFromDescriptor(antigravityDescriptor(true), {
+      env: {},
+      home,
+      existsSync,
+    });
+    assert.strictEqual(result, cliDir, 'GSD-marked cli dir must win over bare-existing legacy dir');
+  });
+
+  test('coexistence WITHOUT probeExists still shadows to legacy (documents the pre-fix behavior)', () => {
+    const home = '/home/u';
+    const cliDir = path.join(home, '.gemini', 'antigravity-cli');
+    const legacyDir = path.join(home, '.gemini', 'antigravity');
+    const existsSync = (p) => p === cliDir || p === legacyDir;
+    const result = resolveConfigHomeFromDescriptor(antigravityDescriptor(false), {
+      env: {},
+      home,
+      existsSync,
+    });
+    // No marker → legacy first-bare-existing wins. This is exactly the #217 bug
+    // and proves probeExists is the load-bearing fix.
+    assert.strictEqual(result, legacyDir);
+  });
+
+  test('coexistence: legacy + ide both exist, only ide is GSD-marked → returns antigravity-ide', () => {
+    const home = '/home/u';
+    const ideDir = path.join(home, '.gemini', 'antigravity-ide');
+    const legacyDir = path.join(home, '.gemini', 'antigravity');
+    const markerPath = path.join(ideDir, AG_MARKER);
+    const existsSync = (p) => p === markerPath || p === ideDir || p === legacyDir;
+    const result = resolveConfigHomeFromDescriptor(antigravityDescriptor(true), {
+      env: {},
+      home,
+      existsSync,
+    });
+    assert.strictEqual(result, ideDir);
+  });
+
+  test('marker on legacy dir: GSD lives in legacy antigravity (a real 1.x install) → returns legacy even when cli dir exists bare', () => {
+    const home = '/home/u';
+    const legacyDir = path.join(home, '.gemini', 'antigravity');
+    const cliDir = path.join(home, '.gemini', 'antigravity-cli');
+    const markerPath = path.join(legacyDir, AG_MARKER);
+    // Legacy carries the marker; cli dir exists but is not GSD's. Legacy wins.
+    const existsSync = (p) => p === markerPath || p === legacyDir || p === cliDir;
+    const result = resolveConfigHomeFromDescriptor(antigravityDescriptor(true), {
+      env: {},
+      home,
+      existsSync,
+    });
+    assert.strictEqual(result, legacyDir);
+  });
+
+  test('no marker anywhere (dirs exist but no GSD installed yet): falls back to bare-existence first match', () => {
+    const home = '/home/u';
+    const ideDir = path.join(home, '.gemini', 'antigravity-ide');
+    // Only ide dir exists, no gsd-core/VERSION anywhere → pass 2 returns ide.
+    const existsSync = (p) => p === ideDir;
+    const result = resolveConfigHomeFromDescriptor(antigravityDescriptor(true), {
+      env: {},
+      home,
+      existsSync,
+    });
+    assert.strictEqual(result, ideDir, 'with no marker, bare-existence pass still resolves the single existing 2.x dir');
+  });
+
+  test('probeExists present but nothing exists → fallback to probe[0] (legacy default preserved)', () => {
+    const home = '/home/u';
+    const result = resolveConfigHomeFromDescriptor(antigravityDescriptor(true), {
+      env: {},
+      home,
+      existsSync: () => false,
+    });
+    assert.strictEqual(result, path.join(home, '.gemini', 'antigravity'));
+  });
+
   test('antigravity: ANTIGRAVITY_CONFIG_DIR env override wins over any probe', () => {
     const result = resolveConfigHomeFromDescriptor(
       {
@@ -421,6 +525,67 @@ describe('descriptor-driven equivalence: dot-home-nested antigravity probe hit/m
   });
 });
 
+// ── #213/#217 thread-4: existing-install ambiguity detector ───────────────────
+describe('detectAntigravityDirAmbiguity (migration/operator-guidance signal)', () => {
+  const HOMEU = '/home/u';
+  const dir = (name) => path.join(HOMEU, '.gemini', name);
+  const markerOf = (name) => path.join(dir(name), 'gsd-core', 'VERSION');
+
+  test('single dir present → not ambiguous', () => {
+    const cli = dir('antigravity-cli');
+    const r = detectAntigravityDirAmbiguity({
+      env: {},
+      home: HOMEU,
+      existsSync: (p) => p === cli || p === markerOf('antigravity-cli'),
+    });
+    assert.strictEqual(r.ambiguous, false);
+    assert.strictEqual(r.resolved, cli);
+    assert.deepStrictEqual(r.presentDirs, [cli]);
+    assert.deepStrictEqual(r.gsdMarkedDirs, [cli]);
+    assert.strictEqual(r.envOverridden, false);
+  });
+
+  test('legacy + cli both present, GSD marked in cli → ambiguous, resolves to cli', () => {
+    const legacy = dir('antigravity');
+    const cli = dir('antigravity-cli');
+    const r = detectAntigravityDirAmbiguity({
+      env: {},
+      home: HOMEU,
+      existsSync: (p) => p === legacy || p === cli || p === markerOf('antigravity-cli'),
+    });
+    assert.strictEqual(r.ambiguous, true, 'two probe dirs present must flag ambiguity');
+    assert.strictEqual(r.resolved, cli, 'marker disambiguates resolution to cli');
+    assert.deepStrictEqual(r.presentDirs.sort(), [legacy, cli].sort());
+    assert.deepStrictEqual(r.gsdMarkedDirs, [cli]);
+  });
+
+  test('misinstall surface: legacy + cli present but GSD marked ONLY in legacy → ambiguous, resolves to legacy', () => {
+    // This is exactly the #217 victim: GSD was written into the legacy/IDE dir,
+    // so the marker is in legacy and the resolver keeps it there. The detector
+    // flags ambiguity so the installer/update can prompt the operator.
+    const legacy = dir('antigravity');
+    const cli = dir('antigravity-cli');
+    const r = detectAntigravityDirAmbiguity({
+      env: {},
+      home: HOMEU,
+      existsSync: (p) => p === legacy || p === cli || p === markerOf('antigravity'),
+    });
+    assert.strictEqual(r.ambiguous, true);
+    assert.strictEqual(r.resolved, legacy);
+    assert.deepStrictEqual(r.gsdMarkedDirs, [legacy]);
+  });
+
+  test('env override short-circuits: envOverridden flag set when ANTIGRAVITY_CONFIG_DIR present', () => {
+    const r = detectAntigravityDirAmbiguity({
+      env: { ANTIGRAVITY_CONFIG_DIR: '/custom/ag' },
+      home: HOMEU,
+      existsSync: () => true,
+    });
+    assert.strictEqual(r.envOverridden, true);
+    assert.strictEqual(r.resolved, '/custom/ag', 'env override wins over probe entirely');
+  });
+});
+
 // ── GOLDEN GENERIC-AGENTS-ROOT (kimi probe) ───────────────────────────────────
 
 describe('descriptor-driven equivalence: generic-agents-root kimi probe hit/miss', () => {
diff --git a/tests/runtime-homes.property.test.cjs b/tests/runtime-homes.property.test.cjs
new file mode 100644
index 000000000..73a436d2f
--- /dev/null
+++ b/tests/runtime-homes.property.test.cjs
@@ -0,0 +1,127 @@
+'use strict';
+
+/**
+ * Property-based tests for runtime-homes.cjs dot-home-nested probe resolution.
+ *
+ * Module: gsd-core/bin/lib/runtime-homes.cjs
+ * Exported: resolveConfigHomeFromDescriptor(descriptor, opts)
+ *
+ * `resolveConfigHomeFromDescriptor` (dot-home-nested kind) is a deterministic
+ * transformation: (descriptor + filesystem-existence state) → resolved path.
+ * Per RULESET.TESTS.property-based-testing it carries an invariant worth
+ * pinning across randomized existence/marker combinations — especially the
+ * #213/#217 `probeExists` marker-priority branch.
+ *
+ * Properties tested:
+ *   (a) Membership: the resolved dir is ALWAYS one of `base/<candidate>` for
+ *       some candidate in `probe` (never an off-list path).
+ *   (b) Precedence: resolution follows the documented order —
+ *       first marked candidate (when probeExists set) → first bare-existing
+ *       candidate → `probe[0]` fallback.
+ */
+
+const { describe, test } = require('node:test');
+const assert = require('node:assert/strict');
+const path = require('node:path');
+const fc = require('./helpers/fast-check-setup.cjs');
+
+const { resolveConfigHomeFromDescriptor } = require(
+  path.join(__dirname, '..', 'gsd-core', 'bin', 'lib', 'runtime-homes.cjs'),
+);
+
+const MARKER = 'gsd-core/VERSION';
+const CANDIDATE_POOL = ['antigravity', 'antigravity-ide', 'antigravity-cli', 'foo', 'bar'];
+
+describe('runtime-homes: dot-home-nested probe resolution properties', () => {
+  test('property: resolved dir is always a probe candidate, in documented precedence', () => {
+    fc.assert(
+      fc.property(
+        fc.record({
+          home: fc.constantFrom('/home/u', '/Users/x', '/root', '/srv/app'),
+          probe: fc.uniqueArray(fc.constantFrom(...CANDIDATE_POOL), { minLength: 1, maxLength: 5 }),
+          useMarker: fc.boolean(),
+          existMask: fc.array(fc.boolean(), { minLength: 5, maxLength: 5 }),
+          markMask: fc.array(fc.boolean(), { minLength: 5, maxLength: 5 }),
+        }),
+        ({ home, probe, useMarker, existMask, markMask }) => {
+          const parent = '.gemini';
+          const base = path.join(home, parent);
+          const candDir = (c) => path.join(base, c);
+
+          // Which candidate dirs exist on disk, and which carry the marker.
+          // A marker only matters where the dir itself exists (realistic install).
+          const exists = new Set();
+          const marked = new Set();
+          probe.forEach((c, i) => {
+            if (existMask[i]) exists.add(candDir(c));
+            if (useMarker && markMask[i] && existMask[i]) marked.add(candDir(c));
+          });
+
+          const existsSync = (p) =>
+            exists.has(p) || [...marked].some((d) => p === path.join(d, MARKER));
+
+          const descriptor = {
+            kind: 'dot-home-nested',
+            name: 'antigravity',
+            parent,
+            env: ['ANTIGRAVITY_CONFIG_DIR'],
+            probe,
+          };
+          if (useMarker) descriptor.probeExists = MARKER;
+
+          const result = resolveConfigHomeFromDescriptor(descriptor, {
+            env: {},
+            home,
+            existsSync,
+          });
+
+          // (a) Membership invariant.
+          const allCandidateDirs = probe.map(candDir);
+          assert.ok(
+            allCandidateDirs.includes(result),
+            `result ${result} must be one of ${JSON.stringify(allCandidateDirs)}`,
+          );
+
+          // (b) Precedence oracle: first marked → first bare-existing → probe[0].
+          const firstMarked = allCandidateDirs.find((d) => marked.has(d));
+          const firstExisting = allCandidateDirs.find((d) => exists.has(d));
+          const expected =
+            (useMarker && firstMarked) || firstExisting || candDir(probe[0]);
+          assert.equal(result, expected);
+        },
+      ),
+    );
+  });
+
+  test('property: an env override always wins over any probe/marker state', () => {
+    fc.assert(
+      fc.property(
+        fc.record({
+          home: fc.constantFrom('/home/u', '/root'),
+          // Absolute overrides only: the resolver's env branch tilde-expands
+          // against the real os.homedir(), so a '~/' case would not be hermetic.
+          override: fc.constantFrom('/custom/ag', '/opt/x', '/var/data/ag'),
+          probe: fc.uniqueArray(fc.constantFrom(...CANDIDATE_POOL), { minLength: 1, maxLength: 5 }),
+          useMarker: fc.boolean(),
+        }),
+        ({ home, override, probe, useMarker }) => {
+          const descriptor = {
+            kind: 'dot-home-nested',
+            name: 'antigravity',
+            parent: '.gemini',
+            env: ['ANTIGRAVITY_CONFIG_DIR'],
+            probe,
+          };
+          if (useMarker) descriptor.probeExists = MARKER;
+
+          const result = resolveConfigHomeFromDescriptor(descriptor, {
+            env: { ANTIGRAVITY_CONFIG_DIR: override },
+            home,
+            existsSync: () => true, // every dir + marker "exists" — override must still win
+          });
+          assert.equal(result, override);
+        },
+      ),
+    );
+  });
+});