feat(project): add Gemini project skills and MCP installation

docs/plans/project-install-e2e/client-plans.md

@@ -260,6 +260,17 @@ malformed/commented settings, conflicting user server and trust gating. A
 settings-file receipt proves configuration, not initialized MCP/tools or
 authentication. No extension install/global profile redirection is needed.
 
+**Implemented checkpoint (2026-10-23).** `65b8f17a` qualifies the native
+project component lane with independent implementation
+[R1](gemini-code-review-r1.md) and [R2](gemini-code-review-r2.md) GO. Project
+configuration success remains prepared with installed exact objects. Native
+session discovery, workspace trust, system policy and MCP initialization remain
+unobserved; activation attestation cannot upgrade that status. Bounded
+user/workspace restriction and alias warnings preserve policy and foreign
+files. [Pinned evidence and verification](gemini-implementation-evidence.md)
+separate actual version/help research, production composition contracts and
+remaining hosted native runtime qualification.
+
 ## 5. OpenCode — project config at repository root
 
 **Evidence/choice.** Native project MCP uses `<project>/opencode.json` or
@@ -590,7 +601,7 @@ is replaced by explicit unsupported. R2 fixes independently verified GO in
 | claude | GO | Verified | GO | Root assignment required |
 | codex | GO | Verified | GO | Root assignment required |
 | cursor | GO | Verified | GO | Root assignment required |
-| gemini | GO | Verified | GO | Root assignment required |
+| gemini | GO | Verified | GO | Implemented at65b8f17a; independent implementation R1/R2 GO; native discovery pending |
 | opencode | GO | Verified | GO | Root assignment required |
 | copilot | GO | Verified | GO | Root assignment required |
 | kiro | GO | Verified | GO | Root assignment required |

docs/plans/project-install-e2e/gemini-code-review-r1.md

@@ -0,0 +1,37 @@
+# Gemini project implementation independent review R1
+
+Reviewer: project_core, 2026-10-23. Initial read-only checkpoint `d76f29ae..a96b4aff07dedfb99297d3fab564b1c778d6968b` in the Gemini child worktree. Review scope is the Gemini adapter and the owner-authorized precise CodecGemini comment parsing delta. Shared core was reviewed separately.
+
+## Decision
+
+**R1 GO at final frozen `65b8f17a951e80f06f9ed9c2677dd16a3ccd3d0a`.** Scoped root selection, conservative project readiness, exact native ownership and the precise Gemini comment codec changes have no confirmed blocker. Initial checkpoint observations below are retained as review history. Native Gemini session discovery and cohesive source/project CLI execution remain separate qualification/integration gates.
+
+## Initial checkpoint assessment
+
+**No confirmed blocker in the scoped native paths or codec delta. Final GO is pending the author's catalog qualification, conservative project readiness, disabled/shadowed settings, alias/preflight and composed stager tests.** The initial checkpoint alone is not yet project admission/product proof.
+
+- Project native settings/skills root is explicitly `<TargetContext.ProjectRoot>/.gemini`. Detected `Client.ConfigRoot` remains the original user profile. Project/root mismatch and changed original user context are rejected before native operations.
+- Native mutation, verification, removal and registry inspection select the same explicit root; removal is supplied the recorded actual native registry and TargetContext. Exact existing ownership codecs and native skill transactions are reused.
+- The managed artifact layout stays under the selected project, with physical profile canonicalization and no-follow containment reused. User home variables are not replaced and host trust is not granted.
+- `CodecGemini` settings.json accepts comments while preserving the existing AST and exact entry receipts. Duplicate keys, malformed input and trailing commas remain errors. Other strict JSON codecs stay strict.
+- Independently inspected hujson's parser representation: a final child Value.AfterExtra is cleared for a closing delimiter without a trailing comma and remains present when a trailing comma exists; the new sentinel check therefore does distinguish this format boundary while retaining comments.
+- Remaining direct parseDocument calls in transition*.go are guarded closed OpenCode dialect transitions. They do not admit CodecGemini, so no unrelated transition broadening is needed.
+
+## Final review checklist
+
+Review the final scoped policy/catalog and readiness delta, run the full Gemini and nativeconfig packages independently on the frozen tree, and verify user behavior plus scoped isolation/disabled/foreign-edit/collision/alias/attestation boundaries. A cohesive composed source/project lifecycle follows integration; adapter fixture proof must not be labeled native Gemini process certification.
+
+## Final frozen checkpoint verification
+
+Reviewed the exact final tree read-only, including the real core merge, Gemini catalog qualification and project policy, all moved composed contracts in the external providers test package, and the final `document.go` / `gemini_document.go` last-member deletion correction.
+
+- The catalog qualifies only Gemini project scope through its declared native-config lifecycle. It does not select a test constructor or alter the user lifecycle traits.
+- Project filesystem success consistently remains ActivationPrepared plus VerificationInstalled, without activation attestation. Neither repeated automatic reconciliation, verify-only, a restart, ambient trust variables nor `--activation-complete` can claim native session discovery. The existing ActivationPreflighter rejects the shortcut before mutation and direct adapter reuse invokes the same guard.
+- Preflight reads user/project settings through the exact comment-aware native kernel, preserves disabled skills and MCP restrictions, and reports possible `.agents/skills` shadowing. Workspace trust, system policy and MCP initialization remain explicitly unobserved; there is no new trust/settings engine.
+- The composed loader/planner/renderer/stager/activator contract renders portable commands as Gemini skills and installs/removes the exact skill/command/MCP objects under the project root. Foreign entries/comments, user profile and project B remain unchanged. Malformed settings, object collisions, writer-lock failure, scope/root mismatch and changed original user context fail closed.
+- The final codec fix removes only trailing commas created by deleting a last managed member, moves surviving foreign trivia to the enclosing delimiter, and revalidates the comment-only document. Native-invalid input trailing commas still fail; unrelated strict JSON codecs remain unchanged. The foreign-trivia regression exercises the problematic preceding member directly.
+- Architecture was preserved by moving composed journey tests to `providers/project_gemini_*_test.go`, package providers_test; no upward-import suppression was added.
+
+Independent final execution (`-count=1 -p=2 -timeout=2m`): full Gemini **PASS 0.046s**, full nativeconfig **PASS 3.730s**, full domain **PASS 0.034s**, and providers `^TestProjectGemini` **PASS 0.061s**. The authored CI lint evidence records both exact changed-code and full-file size/architecture gates at zero issues. Shared core CI now discovers TestProject contracts in nativeconfig, providers and all client packages on Linux, macOS and Windows.
+
+No confirmed review finding remains open. These are inert fixture/contract checks, not hosted native Gemini product certification.

docs/plans/project-install-e2e/gemini-code-review-r2.md

@@ -0,0 +1,32 @@
+# Gemini project implementation independent review R2
+
+Reviewer: sources_lead, 2026-10-23. Reviewed exact frozen commit `65b8f17a951e80f06f9ed9c2677dd16a3ccd3d0a` read-only, cumulatively against the reviewed project core. No Gemini worker files were changed.
+
+## Decision
+
+**R2 GO.** No confirmed implementation blocker remains in the Gemini project adapter, bounded settings-policy warnings or precise native-config comment parser. This qualifies the implemented file and lifecycle contracts; native Gemini session discovery, workspace trust, system policy and MCP initialization remain explicitly unobserved. Combined source/project CLI qualification follows integration.
+
+## Independent review findings
+
+- Project selection consistently uses the explicit TargetContext root for planning, registry inspection, native object preparation, activation, verification and removal. Original detected user configuration remains separate. Changed user authority, user registry substitution and managed-root escape fail closed through existing contextual physical-path checks.
+- The domain catalog exposes the project native-config component lane without altering user lifecycle traits. The production loader/planner/command renderer/stager/activator composition is exercised by external provider tests; no test-only adapter composition is required.
+- Project file success is consistently `ActivationPrepared` and `VerificationInstalled` with `ActivationAttested=false`. Repeated automatic reconciliation and verify-only do not promote readiness. The shared ActivationPreflighter runs before generic activation attestation, and direct adapter reuse also rejects that shortcut before mutation. An ambient trust flag is not accepted as discovery evidence.
+- Preserved user/workspace restrictions and a same-name `.agents/skills` alias generate bounded warnings. These checks do not write trust or policy and do not claim to reconstruct Gemini's complete settings engine. System policy and MCP initialization remain explicitly unobserved.
+- Native entry receipts and exact skill ownership remain the mutation authority. Project A add/repeat/verify/remove preserves user configuration, project B, foreign skills, foreign MCP entries, settings and comments. Foreign same-name collisions, malformed settings and writer-lock failure leave native state unchanged; removal is repeatable and exact.
+- CodecGemini accepts the pinned native format's comments without admitting duplicate keys or input trailing commas. The deletion correction removes only renderer-created trailing commas and preserves surviving foreign trivia. Strict JSON codecs retain their prior parser. Existing OpenCode-only transitions are unaffected.
+- Reviewed pinned v0.65.0 release evidence, configuration/help boundaries and the documented original user-root handling. The implementation makes no live-session, model, authentication or native trust claim from these contract tests.
+
+## Independent execution
+
+Executed against the exact clean frozen tree with `-count=1 -p=2`:
+
+| Scope | Result |
+| --- | --- |
+| Full clients/gemini package | PASS, 0.028s |
+| Full adapters/nativeconfig package | PASS, 3.570s |
+| Full domain package | PASS, 0.023s |
+| Providers `^TestProjectGemini` composition contracts | PASS, 0.072s |
+
+The composed tests cover rendered command skills, MCP and skills, prepared status, attestation rejection, original user context, other-project isolation, restrictions/alias preservation, exact removal, malformed input, collision and rollback. No package payload, model request or MCP server was executed. The hosted native runtime guard remains unchanged.
+
+No review correction was requested in this rotation.

docs/plans/project-install-e2e/gemini-implementation-evidence.md

@@ -0,0 +1,88 @@
+# Gemini project component implementation evidence
+
+Date: 2026-10-23. Implemented frozen code: `65b8f17a`. The selected lane installs
+native project skills and MCP configuration; it does not invent a project
+extension registry. Independent implementation [R1](gemini-code-review-r1.md)
+and [R2](gemini-code-review-r2.md) both grant GO for the bounded file and
+lifecycle contracts.
+
+## Pre-code official artifact and help research
+
+Official [Gemini CLI v0.65.0 release bundle](https://github.com/google-gemini/gemini-cli/releases/download/v0.65.0/gemini-cli-bundle.zip):
+21,215,960 bytes; SHA256
+`bb5e7e879608bd9b3fe261930d3886fa56aacbf471da1655f2978eb35b705a73`.
+The artifact checksum was verified before implementation. Actual read-only
+version, skills help and MCP help probes ran with no network, no user mounts
+and fresh isolated home/project directories. The version reports `0.65.0`;
+skills help exposes list, enable, disable, install and uninstall; MCP help
+exposes add, remove, list, enable and disable. These observations establish the
+pinned help/schema research boundary, not project session discovery.
+
+Primary documentation:
+[configuration](https://geminicli.com/docs/reference/configuration/),
+[skills](https://geminicli.com/docs/cli/skills/), and
+[trusted folders](https://geminicli.com/docs/cli/trusted-folders/).
+
+Read-only inspection of the exact released JavaScript bundle establishes:
+
+- `chunk-AZOL6UFL.js`: project settings are `.gemini/settings.json`; trust gates
+  workspace merging between user and system settings (`mergeSettings`, around
+  line16338). The pinned schema defaults folder trust to true, resolving stale
+  text in the separate trusted-folders page.
+- The same chunk defines `mcpServers` named-entry shallow merge around
+  line12455; `mcp.allowed`/`mcp.excluded` around line13987; skills enabled and
+  union-merged disabled names around line14692; admin MCP/skills enabled fields
+  around lines15098/15148. Admin sections use replace merging.
+- Native settings parse JSON after stripping comments. Comments are accepted;
+  input trailing commas remain invalid.
+- `chunk-DPTJ5QZL.js`: original user configuration and trust storage stay under
+  native user authority. Workspace `.agents/skills` is a higher-priority alias
+  at the workspace tier; neither HOME nor GEMINI_CLI_HOME is rebound to the
+  project by this implementation.
+
+Offsets identify this immutable bundle and are not claims about future native
+versions. No package payload, MCP server or model request was executed during
+these probes.
+
+## Implemented contract and limits
+
+Planning, inspection, activation, verification and removal use the actual
+selected project `.gemini` root while retaining detected user ConfigRoot.
+Managed artifacts remain separately under project `.uap`. Exact MCP receipts,
+skill directory ownership, rollback and no-follow/canonical path checks are
+reused. Comment-aware Gemini writes preserve foreign entries/trivia; duplicate
+keys and trailing commas remain invalid, and other strict JSON codecs retain
+their previous parser.
+
+Every configuration-only project success is `ActivationPrepared` plus
+`VerificationInstalled`, with no activation attestation. Repeat automatic
+reconciliation and read-only verification do not claim native discovery. The
+existing preflight port rejects `--activation-complete` before the generic
+shortcut, including direct adapter reuse. An ambient trust bypass flag is not
+discovery evidence. Trust and policy files are never changed.
+
+Warnings inspect configured user/workspace restrictions and potential
+same-name `.agents/skills` alias paths. They do not recreate Gemini's full
+settings engine. Session discovery, workspace trust, system policy and MCP
+initialization remain explicitly unobserved. The existing user-scope lifecycle
+stays unchanged.
+
+## Verification
+
+Production loader, planner, portable command renderer, stager and activator
+contracts deliver ordinary skills, command skills and MCP entries into project
+A; original user and project B byte/mode inventories remain unchanged. Tests
+cover repeated activation/verification, exact repeatable remove, preserved
+restrictions/alias, malformed settings, foreign same-name collision, and an MCP
+writer failure after skill installation with complete skill rollback.
+
+Author's exact Go1.26.10 checks: composed project contracts PASS0.063s;
+native codec project contracts PASS0.008s; full Gemini/nativeconfig/domain
+PASS0.028s/3.790s/0.040s. Exact golangci-lint2.13.2 changed-code and whole-file
+size/complexity/architecture gates both report zero issues. Both independent
+reviewers separately ran the frozen packages and composed tests successfully.
+
+These are inert transport-independent file/composition contracts. Real Gemini
+project skills/MCP listing from A plus a fresh session, and the cohesive
+source/project CLI scenario, remain separate hosted qualification/integration
+gates. The existing hosted-only native runtime guard remains unchanged.

install/integrationctl/agentplugins/adapters/nativeconfig/document.go

@@ -12,9 +12,10 @@ import (
 )
 
 type document struct {
-	ast   hujson.Value
-	root  *hujson.Object
-	jsonc bool
+	ast          hujson.Value
+	root         *hujson.Object
+	jsonc        bool
+	commentsOnly bool
 }
 
 func parseDocument(body []byte, jsonc bool) (*document, error) {
@@ -35,7 +36,9 @@ func parseDocument(body []byte, jsonc bool) (*document, error) {
 	return &document{ast: ast, root: root, jsonc: jsonc}, nil
 }
 
-func newDocument(jsonc bool) (*document, error) { return parseDocument([]byte("{}\n"), jsonc) }
+func newDocument(jsonc bool, codec Codec) (*document, error) {
+	return parseCodecDocument([]byte("{}\n"), jsonc, codec)
+}
 
 func rejectDuplicateKeys(value *hujson.Value, path string) error {
 	switch node := value.Value.(type) {
@@ -146,11 +149,20 @@ func removeEntry(obj *hujson.Object, name string) bool {
 }
 
 func (doc *document) render() ([]byte, error) {
+	if doc.commentsOnly {
+		geminiRemoveTrailingCommas(&doc.ast)
+	}
 	body := doc.ast.Pack()
 	if !doc.jsonc && !json.Valid(body) {
 		return nil, fmt.Errorf("rendered native config is not strict JSON")
 	}
-	if _, err := parseDocument(body, doc.jsonc); err != nil {
+	var err error
+	if doc.commentsOnly {
+		_, err = parseCodecDocument(body, false, CodecGemini)
+	} else {
+		_, err = parseDocument(body, doc.jsonc)
+	}
+	if err != nil {
 		return nil, fmt.Errorf("validate rendered native config: %w", err)
 	}
 	return body, nil