@skillcap/gdh 0.17.0 → 0.17.2

package/INSTALL-BUNDLE.json

@@ -1,5 +1,5 @@
 {
   "product": "GDH",
-  "version": "0.17.0",
+  "version": "0.17.2",
   "installMode": "packaged_install"
 }

package/RELEASE-SPAN-UPDATE-CONTRACTS.json

@@ -1356,6 +1356,121 @@
           }
         ]
       }
+    },
+    {
+      "version": "0.17.1",
+      "releaseTag": "v0.17.1",
+      "migrationStatus": "no_op",
+      "summary": "v0.17.1 fixes update and migration follow-through classification plus managed Godot LSP startup timing without changing managed project surface versions. Existing targets do not need release-scoped migration for this patch line; agents should follow the ordinary self-update terminal contract, and managed LSP state remains compatible.",
+      "releaseHighlights": {
+        "summary": "v0.17.1 fixes two dogfooding regressions from the v0.17.0 authoring release. Update and migration follow-up now separates safe GDH-managed repair from project-owned manual review, and managed Godot LSP startup now waits long enough for slower real projects to become protocol-ready.",
+        "operatorChanges": [
+          "**Self-update no longer hides safe repair behind manual review.** `gdh self-update` and `gdh migrate --apply` can repair auto-applicable managed bridge drift even when project-owned rules still need review.",
+          "**Terminal commands are safer to trust.** `terminal.commands` now contains only GDH-classified auto-applicable follow-up commands; project-owned review remains in `terminal.manualSteps`.",
+          "**Generated update guidance is clearer.** `/gdh-update` and `/gdh-migrate` tell agents to run surfaced safe commands before stopping for manual review.",
+          "**Migration action hints point at apply when work is auto-applicable.** Lifecycle surfaces that GDH can safely migrate now surface `gdh migrate --apply` instead of preview-only `gdh migrate`.",
+          "**Managed LSP startup is less brittle.** GDH now gives the Godot editor a longer startup window, retries startup `initialize` timeouts, and records command, pid, port, timeout budget, attempts, elapsed time, and protocol failure details when authoring LSP still cannot become ready.",
+          "**Real-project LSP proof is restored.** The Beacon dogfood target now reaches `authoring.lsp` `ready` with initialized protocol health using the local v0.17.1 build."
+        ]
+      },
+      "updateContract": {
+        "summary": "No release-scoped managed migration is required for v0.17.1. After self-update, agents should trust the terminal contract: run any surfaced auto-applicable `terminal.commands`, validate with `terminal.validationCommands`, and stop for the remaining `terminal.manualSteps`. Managed LSP startup behavior improves automatically with the new GDH package and does not require target migration.",
+        "steps": [
+          {
+            "id": "verify_post_update_terminal",
+            "kind": "mechanical",
+            "summary": "Read the post-update terminal result.",
+            "detail": "After `gdh self-update`, inspect `terminal.state`, `terminal.commands`, `terminal.validationCommands`, and `terminal.manualSteps`. Treat `terminal.commands` as GDH-classified auto-applicable follow-up only.",
+            "commands": [
+              "gdh status"
+            ],
+            "validationCommands": [
+              "gdh status"
+            ]
+          },
+          {
+            "id": "run_safe_terminal_commands",
+            "kind": "mechanical",
+            "summary": "Run surfaced safe commands before manual review.",
+            "detail": "If `terminal.commands` is non-empty, run those commands because GDH classified them as auto-applicable. This may include managed bridge repair or migration apply work that is independent from project-owned review.",
+            "commands": [
+              "gdh migrate --apply",
+              "gdh bridge repair"
+            ],
+            "validationCommands": [
+              "gdh status",
+              "gdh bridge status"
+            ]
+          },
+          {
+            "id": "review_remaining_manual_steps",
+            "kind": "manual_review",
+            "summary": "Stop for remaining project-owned or editor-side manual review.",
+            "detail": "If `terminal.manualSteps` remains after safe commands and validation, explain those steps and stop. Do not overwrite project-owned rules or pretend editor-side plugin enable happened automatically.",
+            "commands": [],
+            "validationCommands": [
+              "gdh status"
+            ]
+          }
+        ]
+      }
+    },
+    {
+      "version": "0.17.2",
+      "releaseTag": "v0.17.2",
+      "migrationStatus": "no_op",
+      "summary": "v0.17.2 hardens Codex supported-agent skills and MCP recovery without changing managed project schema or lifecycle surface versions. Existing targets do not need release-scoped schema migration, but Codex targets should run ordinary self-update or adapter repair so skills move to .agents/skills and exact managed legacy .codex/skills copies are removed.",
+      "releaseHighlights": {
+        "summary": "v0.17.2 hardens supported-agent setup after dogfooding exposed Codex skill-location drift and stale MCP registration confusion. Codex target skills now use the documented `.agents/skills` location, exact managed legacy `.codex/skills` files are cleaned up during repair, and MCP recovery guidance now explains what GDH can repair versus what the host agent must reconnect.",
+        "operatorChanges": [
+          "**Codex target skills use the documented project-local location.** Generated GDH target skills now install under `.agents/skills/gdh-*/SKILL.md`.",
+          "**Managed legacy Codex skill copies are cleaned safely.** `gdh adapters install` and migration translation remove exact managed `.codex/skills/gdh-*` files after the new `.agents/skills` copy exists; customized files are preserved.",
+          "**Codex project MCP config is part of readiness.** GDH lifecycle checks now include `.codex/config.toml` alongside Claude `.mcp.json` and Cursor `.cursor/mcp.json`.",
+          "**Codex MCP startup is less ambiguous.** Generated `.codex/config.toml` includes explicit startup and tool timeouts for the GDH MCP server.",
+          "**MCP recovery docs are clearer.** Install/update docs now distinguish project-local repair, Codex user-local registration cleanup, and the host-owned restart needed after a stdio MCP transport closes."
+        ]
+      },
+      "updateContract": {
+        "summary": "No release-scoped managed schema migration is required for v0.17.2. After self-update, Codex users should verify adapter surfaces so generated GDH skills live under `.agents/skills`, exact managed legacy `.codex/skills` copies are gone, and MCP config points at the current pinned GDH command. Closed host MCP transports still require the host agent to reconnect or restart.",
+        "steps": [
+          {
+            "id": "rebake_agent_adapters",
+            "kind": "mechanical",
+            "summary": "Re-bake supported-agent surfaces at the new GDH pin.",
+            "detail": "`gdh self-update` re-runs the adapter install path. If an agent needs to repair surfaces manually, run `gdh adapters install <target>` for repo-local agent surfaces.",
+            "commands": [
+              "gdh adapters install <target>"
+            ],
+            "validationCommands": [
+              "gdh adapters status <target>",
+              "gdh verify drift <target>"
+            ]
+          },
+          {
+            "id": "repair_codex_user_mcp",
+            "kind": "mechanical",
+            "summary": "Repair or remove stale Codex user-local MCP registrations when present.",
+            "detail": "For user-local Codex registrations that point at an old package version or missing legacy launcher, run the GDH Codex user install flow for the expected project key or remove stale unrelated entries with `codex mcp remove <name>`.",
+            "commands": [
+              "gdh adapters install <target> --user --agent codex"
+            ],
+            "validationCommands": [
+              "codex mcp list --json",
+              "gdh adapters status <target>"
+            ]
+          },
+          {
+            "id": "restart_closed_mcp_transport",
+            "kind": "manual_review",
+            "summary": "Restart the host agent session if the live MCP transport is closed.",
+            "detail": "GDH can repair configuration and prove command shape, but Codex, Claude, and Cursor own their live stdio MCP process. If the transport is already closed, refresh or restart the host agent session before trusting MCP tool availability.",
+            "commands": [],
+            "validationCommands": [
+              "gdh adapters status <target>"
+            ]
+          }
+        ]
+      }
     }
   ]
 }

package/node_modules/@gdh/adapters/dist/index.d.ts

@@ -7,27 +7,27 @@ export declare const PROJECT_MCP_RELATIVE_PATH = ".mcp.json";
 export declare const CURSOR_MCP_RELATIVE_PATH = ".cursor/mcp.json";
 export declare const CURSOR_RULE_RELATIVE_PATH = ".cursor/rules/gdh-agent.mdc";
 export declare const CURSOR_ONBOARD_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-onboard/SKILL.md";
-export declare const CODEX_ONBOARD_SKILL_RELATIVE_PATH = ".codex/skills/gdh-onboard/SKILL.md";
+export declare const CODEX_ONBOARD_SKILL_RELATIVE_PATH = ".agents/skills/gdh-onboard/SKILL.md";
 export declare const CLAUDE_STATUS_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/status.md";
 export declare const CLAUDE_MIGRATE_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/migrate.md";
 export declare const CLAUDE_CHECK_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/check.md";
 export declare const CLAUDE_PREPARE_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/prepare.md";
 export declare const CLAUDE_VERIFY_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/verify.md";
-export declare const CODEX_STATUS_SKILL_RELATIVE_PATH = ".codex/skills/gdh-status/SKILL.md";
-export declare const CODEX_MIGRATE_SKILL_RELATIVE_PATH = ".codex/skills/gdh-migrate/SKILL.md";
-export declare const CODEX_CHECK_SKILL_RELATIVE_PATH = ".codex/skills/gdh-check/SKILL.md";
-export declare const CODEX_PREPARE_SKILL_RELATIVE_PATH = ".codex/skills/gdh-prepare/SKILL.md";
-export declare const CODEX_VERIFY_SKILL_RELATIVE_PATH = ".codex/skills/gdh-verify/SKILL.md";
+export declare const CODEX_STATUS_SKILL_RELATIVE_PATH = ".agents/skills/gdh-status/SKILL.md";
+export declare const CODEX_MIGRATE_SKILL_RELATIVE_PATH = ".agents/skills/gdh-migrate/SKILL.md";
+export declare const CODEX_CHECK_SKILL_RELATIVE_PATH = ".agents/skills/gdh-check/SKILL.md";
+export declare const CODEX_PREPARE_SKILL_RELATIVE_PATH = ".agents/skills/gdh-prepare/SKILL.md";
+export declare const CODEX_VERIFY_SKILL_RELATIVE_PATH = ".agents/skills/gdh-verify/SKILL.md";
 export declare const CURSOR_STATUS_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-status/SKILL.md";
 export declare const CURSOR_MIGRATE_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-migrate/SKILL.md";
 export declare const CURSOR_CHECK_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-check/SKILL.md";
 export declare const CURSOR_PREPARE_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-prepare/SKILL.md";
 export declare const CURSOR_VERIFY_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-verify/SKILL.md";
 export declare const CLAUDE_UPDATE_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/update.md";
-export declare const CODEX_UPDATE_SKILL_RELATIVE_PATH = ".codex/skills/gdh-update/SKILL.md";
+export declare const CODEX_UPDATE_SKILL_RELATIVE_PATH = ".agents/skills/gdh-update/SKILL.md";
 export declare const CURSOR_UPDATE_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-update/SKILL.md";
 export declare const CLAUDE_SCAN_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/scan.md";
-export declare const CODEX_SCAN_SKILL_RELATIVE_PATH = ".codex/skills/gdh-scan/SKILL.md";
+export declare const CODEX_SCAN_SKILL_RELATIVE_PATH = ".agents/skills/gdh-scan/SKILL.md";
 export declare const CURSOR_SCAN_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-scan/SKILL.md";
 export declare const LOCAL_PATH_HINTS_RELATIVE_PATH = ".gdh-state/local-paths.json";
 export declare const CODEX_PROJECT_CONFIG_RELATIVE_PATH = ".codex/config.toml";

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package/node_modules/@gdh/adapters/dist/index.js

@@ -40,17 +40,17 @@ export const PROJECT_MCP_RELATIVE_PATH = ".mcp.json";
 export const CURSOR_MCP_RELATIVE_PATH = ".cursor/mcp.json";
 export const CURSOR_RULE_RELATIVE_PATH = ".cursor/rules/gdh-agent.mdc";
 export const CURSOR_ONBOARD_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-onboard/SKILL.md";
-export const CODEX_ONBOARD_SKILL_RELATIVE_PATH = ".codex/skills/gdh-onboard/SKILL.md";
+export const CODEX_ONBOARD_SKILL_RELATIVE_PATH = ".agents/skills/gdh-onboard/SKILL.md";
 export const CLAUDE_STATUS_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/status.md";
 export const CLAUDE_MIGRATE_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/migrate.md";
 export const CLAUDE_CHECK_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/check.md";
 export const CLAUDE_PREPARE_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/prepare.md";
 export const CLAUDE_VERIFY_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/verify.md";
-export const CODEX_STATUS_SKILL_RELATIVE_PATH = ".codex/skills/gdh-status/SKILL.md";
-export const CODEX_MIGRATE_SKILL_RELATIVE_PATH = ".codex/skills/gdh-migrate/SKILL.md";
-export const CODEX_CHECK_SKILL_RELATIVE_PATH = ".codex/skills/gdh-check/SKILL.md";
-export const CODEX_PREPARE_SKILL_RELATIVE_PATH = ".codex/skills/gdh-prepare/SKILL.md";
-export const CODEX_VERIFY_SKILL_RELATIVE_PATH = ".codex/skills/gdh-verify/SKILL.md";
+export const CODEX_STATUS_SKILL_RELATIVE_PATH = ".agents/skills/gdh-status/SKILL.md";
+export const CODEX_MIGRATE_SKILL_RELATIVE_PATH = ".agents/skills/gdh-migrate/SKILL.md";
+export const CODEX_CHECK_SKILL_RELATIVE_PATH = ".agents/skills/gdh-check/SKILL.md";
+export const CODEX_PREPARE_SKILL_RELATIVE_PATH = ".agents/skills/gdh-prepare/SKILL.md";
+export const CODEX_VERIFY_SKILL_RELATIVE_PATH = ".agents/skills/gdh-verify/SKILL.md";
 export const CURSOR_STATUS_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-status/SKILL.md";
 export const CURSOR_MIGRATE_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-migrate/SKILL.md";
 export const CURSOR_CHECK_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-check/SKILL.md";
@@ -63,10 +63,20 @@ export const CURSOR_VERIFY_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-verify/SKIL
 // INTENTIONALLY excluded from VERIFY_DRIFT_SCANNED_FILES (D-13) because the
 // rendered bodies are version-agnostic by design.
 export const CLAUDE_UPDATE_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/update.md";
-export const CODEX_UPDATE_SKILL_RELATIVE_PATH = ".codex/skills/gdh-update/SKILL.md";
+export const CODEX_UPDATE_SKILL_RELATIVE_PATH = ".agents/skills/gdh-update/SKILL.md";
 export const CURSOR_UPDATE_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-update/SKILL.md";
 export const CLAUDE_SCAN_COMMAND_RELATIVE_PATH = ".claude/commands/gdh/scan.md";
-export const CODEX_SCAN_SKILL_RELATIVE_PATH = ".codex/skills/gdh-scan/SKILL.md";
+export const CODEX_SCAN_SKILL_RELATIVE_PATH = ".agents/skills/gdh-scan/SKILL.md";
+const LEGACY_CODEX_SKILL_RELATIVE_PATHS = [
+    [".codex/skills/gdh-onboard/SKILL.md", renderCodexOnboardSkill, "gdh-onboard"],
+    [".codex/skills/gdh-status/SKILL.md", renderCodexStatusSkill, "gdh-status"],
+    [".codex/skills/gdh-migrate/SKILL.md", renderCodexMigrateSkill, "gdh-migrate"],
+    [".codex/skills/gdh-update/SKILL.md", renderCodexUpdateSkill, "gdh-update"],
+    [".codex/skills/gdh-check/SKILL.md", renderCodexCheckSkill, "gdh-check"],
+    [".codex/skills/gdh-prepare/SKILL.md", renderCodexPrepareSkill, "gdh-prepare"],
+    [".codex/skills/gdh-verify/SKILL.md", renderCodexVerifySkill, "gdh-verify"],
+    [".codex/skills/gdh-scan/SKILL.md", renderCodexScanSkill, "gdh-scan"],
+];
 export const CURSOR_SCAN_SKILL_RELATIVE_PATH = ".cursor/skills/gdh-scan/SKILL.md";
 export const LOCAL_PATH_HINTS_RELATIVE_PATH = ".gdh-state/local-paths.json";
 export const CODEX_PROJECT_CONFIG_RELATIVE_PATH = ".codex/config.toml";
@@ -138,6 +148,9 @@ export async function installSupportedAgentAdapters(targetPath, options = {}) {
                 if (action.kind === "ensure_symlink") {
                     await applySymlinkAction(action);
                 }
+                else if (action.kind === "remove_file") {
+                    await applyRemoveFileAction(action);
+                }
                 else if (action.kind === "run_command") {
                     await applyRunCommandAction(action);
                 }
@@ -728,7 +741,7 @@ export function renderClaudeMigrateCommand(pinnedVersion) {
         "5. After apply, read `terminal.state` in the stdout JSON.",
         "6. If `terminal.state` is `healthy`, confirm no further migration action is required and stop.",
         "7. If `terminal.state` is `follow_up_required`, run the surfaced `terminal.commands`, then run the surfaced `terminal.validationCommands`, and confirm the follow-up results before stopping.",
-        "8. If `terminal.state` is `manual_review_required`, explain the surfaced `terminal.manualSteps`, name the surfaced `terminal.validationCommands`, and stop for review instead of improvising a repair.",
+        "8. If `terminal.state` is `manual_review_required`, run any surfaced `terminal.commands` first because they are auto-applicable, then run the surfaced `terminal.validationCommands`, explain the remaining `terminal.manualSteps`, and stop for review instead of improvising a repair.",
         "9. If `terminal.state` is `blocked`, surface `terminal.summary` plus the reasons and stop.",
         "</process>",
         "",
@@ -773,7 +786,7 @@ export function renderCodexMigrateSkill(pinnedVersion) {
         "- after apply, read `terminal.state` in the stdout JSON",
         "- if `terminal.state` is `healthy`, confirm no further migration action is required and stop",
         "- if `terminal.state` is `follow_up_required`, run the surfaced `terminal.commands`, then run the surfaced `terminal.validationCommands`, and confirm the follow-up results before stopping",
-        "- if `terminal.state` is `manual_review_required`, explain the surfaced `terminal.manualSteps`, name the surfaced `terminal.validationCommands`, and stop for review instead of improvising a repair",
+        "- if `terminal.state` is `manual_review_required`, run any surfaced `terminal.commands` first because they are auto-applicable, then run the surfaced `terminal.validationCommands`, explain the remaining `terminal.manualSteps`, and stop for review instead of improvising a repair",
         "- if `terminal.state` is `blocked`, surface `terminal.summary` plus the reasons and stop",
         "</process>",
         "",
@@ -816,7 +829,7 @@ export function renderCursorMigrateSkill(pinnedVersion) {
         "- after apply, read `terminal.state` in the stdout JSON",
         "- if `terminal.state` is `healthy`, confirm no further migration action is required and stop",
         "- if `terminal.state` is `follow_up_required`, run the surfaced `terminal.commands`, then run the surfaced `terminal.validationCommands`, and confirm the follow-up results before stopping",
-        "- if `terminal.state` is `manual_review_required`, explain the surfaced `terminal.manualSteps`, name the surfaced `terminal.validationCommands`, and stop for review instead of improvising a repair",
+        "- if `terminal.state` is `manual_review_required`, run any surfaced `terminal.commands` first because they are auto-applicable, then run the surfaced `terminal.validationCommands`, explain the remaining `terminal.manualSteps`, and stop for review instead of improvising a repair",
         "- if `terminal.state` is `blocked`, surface `terminal.summary` plus the reasons and stop",
         "</process>",
         "",
@@ -880,7 +893,7 @@ export function renderClaudeUpdateCommand(_pinnedVersion) {
         "8. Read `terminal.state` in the apply stdout JSON and treat it as the lifecycle/runtime truth.",
         "9. If `terminal.state` is `healthy`, confirm the update completed and stop.",
         "10. If `terminal.state` is `follow_up_required`, run the surfaced `terminal.commands`, then run the surfaced `terminal.validationCommands`, and confirm the follow-up results before stopping.",
-        "11. If `terminal.state` is `manual_review_required`, explain the surfaced `terminal.manualSteps`, name the surfaced `terminal.validationCommands`, and stop for review instead of inventing a repair.",
+        "11. If `terminal.state` is `manual_review_required`, run any surfaced `terminal.commands` first because they are auto-applicable, then run the surfaced `terminal.validationCommands`, explain the remaining `terminal.manualSteps`, and stop for review instead of inventing a repair.",
         "12. If `terminal.state` is `blocked`, surface `terminal.summary` plus the reasons and stop.",
         "</process>",
         "",
@@ -888,6 +901,7 @@ export function renderClaudeUpdateCommand(_pinnedVersion) {
         "- Do ask for explicit approval after the structured preview and before apply.",
         "- Do not invent migration steps from prose docs; use the machine-readable `preview` payload.",
         "- Do treat `terminal.state` as the primary apply truth; the additive compatibility fields are not the main follow-through contract.",
+        "- `terminal.commands` contains only GDH-classified auto-applicable follow-up; project-owned review stays in `terminal.manualSteps`.",
         "- Bake literal `@latest` in the shellout so the new CLI performs the update, not the old one.",
         "- If `self-update` returns `rolled_back` or `blocked`, surface the failure reason and stop (do not retry).",
         "- If `self-update` returns `skipped_dev_mode`, explain that dev-from-source mode bypasses pinning; no action needed.",
@@ -927,7 +941,7 @@ export function renderCodexUpdateSkill(_pinnedVersion) {
         "8. Read `terminal.state` in the apply stdout JSON and treat it as the lifecycle/runtime truth.",
         "9. If `terminal.state` is `healthy`, confirm the update completed and stop.",
         "10. If `terminal.state` is `follow_up_required`, run the surfaced `terminal.commands`, then run the surfaced `terminal.validationCommands`, and confirm the follow-up results before stopping.",
-        "11. If `terminal.state` is `manual_review_required`, explain the surfaced `terminal.manualSteps`, name the surfaced `terminal.validationCommands`, and stop for review instead of inventing a repair.",
+        "11. If `terminal.state` is `manual_review_required`, run any surfaced `terminal.commands` first because they are auto-applicable, then run the surfaced `terminal.validationCommands`, explain the remaining `terminal.manualSteps`, and stop for review instead of inventing a repair.",
         "12. If `terminal.state` is `blocked`, surface `terminal.summary` plus the reasons and stop.",
         "</process>",
         "",
@@ -935,6 +949,7 @@ export function renderCodexUpdateSkill(_pinnedVersion) {
         "- Do ask for explicit approval after the structured preview and before apply.",
         "- Do not invent migration steps from prose docs; use the machine-readable `preview` payload.",
         "- Do treat `terminal.state` as the primary apply truth; the additive compatibility fields are not the main follow-through contract.",
+        "- `terminal.commands` contains only GDH-classified auto-applicable follow-up; project-owned review stays in `terminal.manualSteps`.",
         "- Bake literal `@latest` in the shellout so the new CLI performs the update, not the old one.",
         "- If `self-update` returns `rolled_back` or `blocked`, surface the failure reason and stop (do not retry).",
         "- If `self-update` returns `skipped_dev_mode`, explain that dev-from-source mode bypasses pinning; no action needed.",
@@ -972,7 +987,7 @@ export function renderCursorUpdateSkill(_pinnedVersion) {
         "8. Read `terminal.state` in the apply stdout JSON and treat it as the lifecycle/runtime truth.",
         "9. If `terminal.state` is `healthy`, confirm the update completed and stop.",
         "10. If `terminal.state` is `follow_up_required`, run the surfaced `terminal.commands`, then run the surfaced `terminal.validationCommands`, and confirm the follow-up results before stopping.",
-        "11. If `terminal.state` is `manual_review_required`, explain the surfaced `terminal.manualSteps`, name the surfaced `terminal.validationCommands`, and stop for review instead of inventing a repair.",
+        "11. If `terminal.state` is `manual_review_required`, run any surfaced `terminal.commands` first because they are auto-applicable, then run the surfaced `terminal.validationCommands`, explain the remaining `terminal.manualSteps`, and stop for review instead of inventing a repair.",
         "12. If `terminal.state` is `blocked`, surface `terminal.summary` plus the reasons and stop.",
         "</process>",
         "",
@@ -980,6 +995,7 @@ export function renderCursorUpdateSkill(_pinnedVersion) {
         "- Do ask for explicit approval after the structured preview and before apply.",
         "- Do not invent migration steps from prose docs; use the machine-readable `preview` payload.",
         "- Do treat `terminal.state` as the primary apply truth; the additive compatibility fields are not the main follow-through contract.",
+        "- `terminal.commands` contains only GDH-classified auto-applicable follow-up; project-owned review stays in `terminal.manualSteps`.",
         "- Bake literal `@latest` in the shellout so the new CLI performs the update, not the old one.",
         "- If `self-update` returns `rolled_back` or `blocked`, surface the failure reason and stop (do not retry).",
         "- If `self-update` returns `skipped_dev_mode`, explain that dev-from-source mode bypasses pinning; no action needed.",
@@ -1563,7 +1579,7 @@ function inspectCodexSkillSurface(targetPath, relativePath, content, expectedCon
             present: content !== null,
             state: content === null ? "missing" : content === expectedContent ? "ready" : "misconfigured",
             summary: content === null
-                ? `Codex \`/${skillName}\` skill is missing and should install under .codex/skills/.`
+                ? `Codex \`/${skillName}\` skill is missing and should install under .agents/skills/.`
                 : content === expectedContent
                     ? `Codex can discover the managed \`/${skillName}\` skill.`
                     : `Codex \`/${skillName}\` skill exists but no longer matches the expected managed GDH skill.`,
@@ -1704,7 +1720,7 @@ async function inspectCodexAdapter(targetPath, guidance, projectMcp, pinnedVersi
                         ? "ready"
                         : "misconfigured",
             summary: codexSkillContent === null
-                ? "Codex onboarding handoff is missing and should install `/gdh-onboard` under .codex/skills/."
+                ? "Codex onboarding handoff is missing and should install `/gdh-onboard` under .agents/skills/."
                 : expectedCodexOnboardSkill === null
                     ? "Codex onboarding handoff cannot be validated yet: no `gdh_version` is pinned (run `gdh setup` or `gdh migrate --apply`)."
                     : codexSkillContent === expectedCodexOnboardSkill
@@ -2196,6 +2212,30 @@ function planCodexRepoInstallActions(targetPath, adapter, pinnedVersion, project
             content: renderManagedCodexProjectConfig(existingContent, pinnedVersion),
         }));
     }
+    actions.push(...planLegacyCodexSkillCleanupActions(targetPath, pinnedVersion));
+    return actions;
+}
+function planLegacyCodexSkillCleanupActions(targetPath, pinnedVersion) {
+    const actions = [];
+    for (const [relativePath, renderFn, skillName] of LEGACY_CODEX_SKILL_RELATIVE_PATHS) {
+        const absolutePath = path.join(targetPath, relativePath);
+        const content = fsSync.existsSync(absolutePath)
+            ? fsSync.readFileSync(absolutePath, "utf8")
+            : null;
+        if (content === null || content !== renderFn(pinnedVersion)) {
+            continue;
+        }
+        actions.push(createInstallAction({
+            agent: "codex",
+            kind: "remove_file",
+            scope: "repo",
+            targetPath,
+            relativePath,
+            state: "planned",
+            mode: "delete",
+            summary: `Remove legacy managed Codex \`/${skillName}\` skill from .codex/skills after installing the documented .agents/skills location.`,
+        }));
+    }
     return actions;
 }
 function planCodexUserInstallActions(targetPath, projectMcp, integrationRootPath, pinnedVersion) {
@@ -2412,6 +2452,12 @@ async function applyWriteFileAction(action) {
     await fs.mkdir(path.dirname(action.absolutePath), { recursive: true });
     await fs.writeFile(action.absolutePath, action.content ?? renderCursorRule(), "utf8");
 }
+async function applyRemoveFileAction(action) {
+    if (action.absolutePath === null) {
+        throw new Error("Remove-file install action is missing an absolute path.");
+    }
+    await fs.rm(action.absolutePath, { force: true });
+}
 async function applyRunCommandAction(action) {
     const [command, ...args] = action.command ?? [];
     if (!command) {
@@ -2509,6 +2555,8 @@ export function renderManagedCodexProjectSection(pinnedVersion) {
         "[mcp_servers.gdh]",
         'command = "npx"',
         `args = ["-y", "@skillcap/gdh@${pinnedVersion}", "mcp", "serve"]`,
+        "startup_timeout_sec = 30",
+        "tool_timeout_sec = 300",
     ].join("\n");
 }
 export function renderManagedCodexProjectConfig(existingContent, pinnedVersion) {
@@ -2753,7 +2801,7 @@ async function inspectProjectConfigLifecycleSurface(targetPath) {
             action: {
                 kind: "apply_migration",
                 summary: "Run GDH migrate to rewrite the project config to the current schema.",
-                command: ["gdh", "migrate", targetPath],
+                command: migrateApplyCommand(targetPath),
                 autoApplicable: true,
             },
         });
@@ -2829,7 +2877,7 @@ async function inspectRulesLifecycleSurface(targetPath) {
             action: {
                 kind: "apply_migration",
                 summary: "Run GDH migrate to create the default rules file for this target.",
-                command: ["gdh", "migrate", targetPath],
+                command: migrateApplyCommand(targetPath),
                 autoApplicable: true,
             },
         });
@@ -2899,7 +2947,7 @@ function inspectAgentContractLifecycleSurface(targetPath, guidanceStatus) {
         action: {
             kind: "apply_migration",
             summary: "Run GDH migrate to merge or refresh the managed agent contract block.",
-            command: ["gdh", "migrate", targetPath],
+            command: migrateApplyCommand(targetPath),
             autoApplicable: true,
         },
     });
@@ -2928,7 +2976,7 @@ async function inspectGuidanceIndexLifecycleSurface(targetPath) {
             action: {
                 kind: "apply_migration",
                 summary: "Run GDH migrate to create the default guidance index for this target.",
-                command: ["gdh", "migrate", targetPath],
+                command: migrateApplyCommand(targetPath),
                 autoApplicable: true,
             },
         });
@@ -2954,7 +3002,7 @@ async function inspectGuidanceIndexLifecycleSurface(targetPath) {
         action: {
             kind: "apply_migration",
             summary: "Run GDH migrate to regenerate the guidance index with updated content.",
-            command: ["gdh", "migrate", targetPath],
+            command: migrateApplyCommand(targetPath),
             autoApplicable: true,
         },
     });
@@ -3011,7 +3059,7 @@ async function inspectGuidanceUnitLifecycleSurface(targetPath, projectConfig) {
             action: {
                 kind: "apply_migration",
                 summary: "Run GDH migrate to create the missing default guidance unit files.",
-                command: ["gdh", "migrate", targetPath],
+                command: migrateApplyCommand(targetPath),
                 autoApplicable: true,
             },
         });
@@ -3026,7 +3074,7 @@ async function inspectGuidanceUnitLifecycleSurface(targetPath, projectConfig) {
         action: {
             kind: "apply_migration",
             summary: "Run GDH migrate to regenerate guidance units with updated content.",
-            command: ["gdh", "migrate", targetPath],
+            command: migrateApplyCommand(targetPath),
             autoApplicable: true,
         },
     });
@@ -3045,7 +3093,8 @@ function inspectMcpManifestLifecycleSurface(targetPath, mcpEnabled, adapterStatu
     }
     const claudeMcp = findAdapterSurface(adapterStatus, "claude", "mcp_file");
     const cursorMcp = findAdapterSurface(adapterStatus, "cursor", "mcp_file");
-    const probes = [claudeMcp, cursorMcp]
+    const codexMcp = findAdapterSurface(adapterStatus, "codex", "mcp_file");
+    const probes = [claudeMcp, cursorMcp, codexMcp]
         .filter((surface) => surface !== null)
         .map((surface) => createVersionProbe({
         targetPath,
@@ -3054,13 +3103,13 @@ function inspectMcpManifestLifecycleSurface(targetPath, mcpEnabled, adapterStatu
         expectedVersion: null,
         detectedVersion: surface.present ? surface.version : null,
     }));
-    const states = [claudeMcp?.state, cursorMcp?.state].filter((state) => state !== undefined);
+    const states = [claudeMcp?.state, cursorMcp?.state, codexMcp?.state].filter((state) => state !== undefined);
     if (states.length > 0 && states.every((state) => state === "ready")) {
         return createLifecycleSurfaceStatus({
             surface: "mcp_manifest",
             management: "managed",
             state: "compatible",
-            summary: "Project MCP config files are aligned for Claude and Cursor.",
+            summary: "Project MCP config files are aligned for Codex, Claude, and Cursor.",
             reasons: [],
             probes,
             action: null,
@@ -3393,7 +3442,7 @@ async function inspectYamlSurfaceDirectory(input) {
             action: {
                 kind: "apply_migration",
                 summary: "Run GDH migrate to normalize legacy runtime surface directories.",
-                command: ["gdh", "migrate", input.targetPath],
+                command: migrateApplyCommand(input.targetPath),
                 autoApplicable: true,
             },
         });
@@ -3433,7 +3482,7 @@ async function inspectYamlSurfaceDirectory(input) {
             action: {
                 kind: "apply_migration",
                 summary: "Run GDH migrate to normalize the affected runtime surfaces.",
-                command: ["gdh", "migrate", input.targetPath],
+                command: migrateApplyCommand(input.targetPath),
                 autoApplicable: true,
             },
         });
@@ -3519,6 +3568,9 @@ function summarizeProjectLifecycleState(state, surfaces) {
 function createLifecycleSurfaceStatus(input) {
     return input;
 }
+function migrateApplyCommand(targetPath) {
+    return ["gdh", "migrate", "--apply", targetPath];
+}
 function createVersionProbe(input) {
     return {
         relativePath: input.relativePath,