trace-to-skill 0.1.63 → 0.1.64

package/README.md

@@ -70,6 +70,7 @@ Use it when you need to:
 - **Report clipboard and pasted-text attachment regressions:** run `trace-to-skill codex-report ./runs` when `Copy as Markdown` disappears, long prompts become `Pasted text.txt`, generated attachments cannot be previewed/edited, or `/goal` treats attached pasted text as empty.
 - **Report deeplink and OAuth launch regressions:** run `trace-to-skill codex-report ./runs` when `codex://oauth_callback`, notification clicks, browser-extension activation, mobile links, or `codex app <path>` fail to route back into Codex.
 - **Diagnose stale connector auth/cache:** run `trace-to-skill codex-report ./runs` when Codex app connectors return `401 Reauthentication required`, keep the same `link_*`, report `isAccessible: false`, or survive restart/plugin reinstall/cache clearing.
+- **Explain missing MCP tools across Codex surfaces:** run `trace-to-skill codex-report ./runs` when MCP servers work in CLI or user-global config but are absent in VS Code, Desktop, WSL, or project-local sessions.
 - **Reduce approval friction:** run `trace-to-skill analyze ./runs` when `Approve for this session` is not remembered, repeated prompts push users toward Full Access, or trusted MCP tools like Playwright require dozens of approvals.
 - **Diagnose sandbox blockers:** run `trace-to-skill analyze ./runs` on Codex traces that fail with sandbox setup refresh, `os error 740`, ACL, ownership, or approval-mode permission errors.
 - **Debug Codex auth/connectivity:** run `trace-to-skill analyze ./runs` on logs with `token_exchange_failed`, `auth.openai.com/oauth/token`, Cloudflare challenge, proxy/CA, IPv6, or stream disconnect symptoms.
@@ -120,6 +121,7 @@ Open-source maintainers do not need more AI-generated noise. They need agents th
 - Did copy/export, long-paste conversion, generated `Pasted text.txt`, or `/goal` attachment handling break the prompt or support-report workflow?
 - Did `codex://` OAuth callbacks, notification clicks, browser-extension launches, mobile pairing links, or `codex app <path>` fail to open the right Codex route?
 - Did a Codex app connector keep stale `link_*` or `isAccessible: false` metadata after `401 Reauthentication required`, restart, plugin reinstall, or cache regeneration?
+- Did MCP servers work in Codex CLI, `~/.codex/config.toml`, or a new conversation, but disappear from VS Code, Desktop, WSL, project `.codex/config.toml`, or an older session?
 - Did repeated approval prompts make a safer scoped mode unusable or require huge per-tool MCP approval configs?
 - Can the failure be reported to OpenAI with line-linked evidence, redaction notes, and the exact diagnostics maintainers need?
 - Can we produce an application-ready OpenAI OSS brief from the repo's actual license, distribution, readiness, and benchmark state?
@@ -198,6 +200,7 @@ Trace analysis detects run-level failures:
 | Sandbox permission | Codex sandbox setup, approval mode, ACL, or workspace ownership blocks tool execution |
 | Codex connectivity | Auth token exchange, proxy/CA, IPv6, Cloudflare challenge, or ChatGPT transport errors block Codex |
 | Codex remote control | Mobile or remote sessions route through stale listeners, stale enrollment, or incomplete helper bundles |
+| Codex MCP discovery mismatch | MCP works in CLI or one config scope but disappears in VS Code, Desktop, WSL, project config, or an older session |
 | Codex MCP runtime | MCP tools are configured but approval, namespace routing, unsupported callable names, or stdio transport fail at runtime |
 | Codex plugin runtime | Browser, Computer Use, Chrome, connectors, or bundled plugins are advertised but fail because helper paths, plugin-list schemas, or cache state drift |
 | Codex file tree UI | Desktop file tree, floating file panel, or file preview cannot be revealed, refreshes stale entries, or loses workspace navigation |
@@ -243,6 +246,7 @@ trace-to-skill demo thinking-hang
 trace-to-skill demo clipboard-attachment
 trace-to-skill demo deeplink-launch
 trace-to-skill demo connector-auth-cache
+trace-to-skill demo mcp-discovery-mismatch
 trace-to-skill demo patch-overwrite
 trace-to-skill guard-patch ./change.patch --root .
 trace-to-skill session-audit ~/.codex --format json
@@ -457,7 +461,7 @@ jobs:
       issues: write
     steps:
       - uses: actions/checkout@v5
-      - uses: grnbtqdbyx-create/trace-to-skill@v0.1.63
+      - uses: grnbtqdbyx-create/trace-to-skill@v0.1.64
         with:
           mode: all
           doctor-threshold: "85"
@@ -506,7 +510,7 @@ Composite action usage:
 
 ```yaml
 - id: trace-to-skill
-  uses: grnbtqdbyx-create/trace-to-skill@v0.1.63
+  uses: grnbtqdbyx-create/trace-to-skill@v0.1.64
   with:
     mode: all
     doctor-threshold: "85"
@@ -548,7 +552,7 @@ Action outputs:
 
 By default, generated reports are also appended to the GitHub Actions Job Summary. Set `job-summary: "false"` to disable that UI output.
 
-Tagged Action releases build and run the CLI from `$GITHUB_ACTION_PATH`, so a workflow pinned to a release tag such as `@v0.1.63` executes that release's checked-out source instead of pulling the default branch at runtime.
+Tagged Action releases build and run the CLI from `$GITHUB_ACTION_PATH`, so a workflow pinned to a release tag such as `@v0.1.64` executes that release's checked-out source instead of pulling the default branch at runtime.
 
 ## Codex Skill
 

package/dist/src/benchmark.js

@@ -126,6 +126,12 @@ const BENCHMARK_CASES = [
         fixture: "fixtures/codex-mcp-runtime.md",
         expectedKinds: ["codex_mcp_runtime", "weak_evidence"]
     },
+    {
+        id: "codex-mcp-discovery-mismatch",
+        title: "Codex MCP discovery and config-scope mismatch",
+        fixture: "fixtures/codex-mcp-discovery-mismatch.md",
+        expectedKinds: ["codex_mcp_discovery_mismatch", "weak_evidence"]
+    },
     {
         id: "codex-plugin-runtime",
         title: "Codex plugin runtime and bundled capability failure",

package/dist/src/benchmark.js.map

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+{"version":3,"file":"benchmark.js","sourceRoot":"","sources":["../../src/benchmark.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AA8B9C,MAAM,eAAe,GAA8B;IACjD;QACE,EAAE,EAAE,qBAAqB;QACzB,KAAK,EAAE,2BAA2B;QAClC,OAAO,EAAE,sBAAsB;QAC/B,aAAa,EAAE,EAAE;QACjB,YAAY,EAAE,IAAI;KACnB;IACD;QACE,EAAE,EAAE,iBAAiB;QACrB,KAAK,EAAE,yCAAyC;QAChD,OAAO,EAAE,wBAAwB;QACjC,aAAa,EAAE,CAAC,cAAc,EAAE,sBAAsB,EAAE,eAAe,EAAE,UAAU,EAAE,mBAAmB,CAAC;QACzG,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,aAAa;QACjB,KAAK,EAAE,4BAA4B;QACnC,OAAO,EAAE,8BAA8B;QACvC,aAAa,EAAE,CAAC,cAAc,EAAE,sBAAsB,EAAE,eAAe,CAAC;QACxE,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,sBAAsB;QAC1B,KAAK,EAAE,mCAAmC;QAC1C,OAAO,EAAE,kCAAkC;QAC3C,aAAa,EAAE,CAAC,sBAAsB,EAAE,oBAAoB,EAAE,eAAe,CAAC;KAC/E;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,kCAAkC;QACzC,OAAO,EAAE,gCAAgC;QACzC,aAAa,EAAE,CAAC,oBAAoB,EAAE,eAAe,CAAC;KACvD;IACD;QACE,EAAE,EAAE,yBAAyB;QAC7B,KAAK,EAAE,0CAA0C;QACjD,OAAO,EAAE,qCAAqC;QAC9C,aAAa,EAAE,CAAC,yBAAyB,EAAE,eAAe,CAAC;KAC5D;IACD;QACE,EAAE,EAAE,0BAA0B;QAC9B,KAAK,EAAE,4CAA4C;QACnD,OAAO,EAAE,sCAAsC;QAC/C,aAAa,EAAE,CAAC,0BAA0B,EAAE,eAAe,CAAC;KAC7D;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,KAAK,EAAE,gCAAgC;QACvC,OAAO,EAAE,iCAAiC;QAC1C,aAAa,EAAE,CAAC,qBAAqB,EAAE,eAAe,CAAC;KACxD;IACD;QACE,EAAE,EAAE,4BAA4B;QAChC,KAAK,EAAE,4DAA4D;QACnE,OAAO,EAAE,wCAAwC;QACjD,aAAa,EAAE,CAAC,4BAA4B,EAAE,eAAe,CAAC;KAC/D;IACD;QACE,EAAE,EAAE,uBAAuB;QAC3B,KAAK,EAAE,gEAAgE;QACvE,OAAO,EAAE,mCAAmC;QAC5C,aAAa,EAAE,CAAC,uBAAuB,EAAE,eAAe,CAAC;KAC1D;IACD;QACE,EAAE,EAAE,4BAA4B;QAChC,KAAK,EAAE,0DAA0D;QACjE,OAAO,EAAE,wCAAwC;QACjD,aAAa,EAAE,CAAC,4BAA4B,EAAE,eAAe,CAAC;KAC/D;IACD;QACE,EAAE,EAAE,yBAAyB;QAC7B,KAAK,EAAE,sDAAsD;QAC7D,OAAO,EAAE,qCAAqC;QAC9C,aAAa,EAAE,CAAC,yBAAyB,EAAE,oBAAoB,EAAE,eAAe,CAAC;KAClF;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,kCAAkC;QACzC,OAAO,EAAE,gCAAgC;QACzC,aAAa,EAAE,CAAC,oBAAoB,EAAE,eAAe,CAAC;KACvD;IACD;QACE,EAAE,EAAE,2BAA2B;QAC/B,KAAK,EAAE,oDAAoD;QAC3D,OAAO,EAAE,uCAAuC;QAChD,aAAa,EAAE,CAAC,2BAA2B,EAAE,oBAAoB,EAAE,sBAAsB,EAAE,eAAe,CAAC;KAC5G;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,qCAAqC;QAC5C,OAAO,EAAE,gCAAgC;QACzC,aAAa,EAAE,CAAC,oBAAoB,EAAE,eAAe,CAAC;KACvD;IACD;QACE,EAAE,EAAE,sBAAsB;QAC1B,KAAK,EAAE,2CAA2C;QAClD,OAAO,EAAE,kCAAkC;QAC3C,aAAa,EAAE,CAAC,sBAAsB,EAAE,eAAe,CAAC;KACzD;IACD;QACE,EAAE,EAAE,gBAAgB;QACpB,KAAK,EAAE,sBAAsB;QAC7B,OAAO,EAAE,4BAA4B;QACrC,aAAa,EAAE,CAAC,gBAAgB,EAAE,eAAe,CAAC;KACnD;IACD;QACE,EAAE,EAAE,UAAU;QACd,KAAK,EAAE,iCAAiC;QACxC,OAAO,EAAE,wBAAwB;QACjC,aAAa,EAAE,CAAC,iBAAiB,EAAE,UAAU,CAAC;QAC9C,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,uBAAuB;QAC3B,KAAK,EAAE,wCAAwC;QAC/C,OAAO,EAAE,mCAAmC;QAC5C,aAAa,EAAE,CAAC,uBAAuB,EAAE,eAAe,CAAC;KAC1D;IACD;QACE,EAAE,EAAE,mBAAmB;QACvB,KAAK,EAAE,2BAA2B;QAClC,OAAO,EAAE,+BAA+B;QACxC,aAAa,EAAE,CAAC,mBAAmB,EAAE,eAAe,CAAC;KACtD;IACD;QACE,EAAE,EAAE,8BAA8B;QAClC,KAAK,EAAE,+CAA+C;QACtD,OAAO,EAAE,0CAA0C;QACnD,aAAa,EAAE,CAAC,8BAA8B,EAAE,eAAe,CAAC;KACjE;IACD;QACE,EAAE,EAAE,sBAAsB;QAC1B,KAAK,EAAE,qDAAqD;QAC5D,OAAO,EAAE,kCAAkC;QAC3C,aAAa,EAAE,CAAC,sBAAsB,EAAE,eAAe,CAAC;KACzD;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,qDAAqD;QAC5D,OAAO,EAAE,gCAAgC;QACzC,aAAa,EAAE,CAAC,oBAAoB,EAAE,eAAe,CAAC;KACvD;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,KAAK,EAAE,wCAAwC;QAC/C,OAAO,EAAE,iCAAiC;QAC1C,aAAa,EAAE,CAAC,qBAAqB,EAAE,eAAe,CAAC;KACxD;IACD;QACE,EAAE,EAAE,kBAAkB;QACtB,KAAK,EAAE,uCAAuC;QAC9C,OAAO,EAAE,8BAA8B;QACvC,aAAa,EAAE,CAAC,kBAAkB,EAAE,eAAe,CAAC;KACrD;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,KAAK,EAAE,yCAAyC;QAChD,OAAO,EAAE,iCAAiC;QAC1C,aAAa,EAAE,CAAC,qBAAqB,EAAE,eAAe,CAAC;KACxD;IACD;QACE,EAAE,EAAE,2BAA2B;QAC/B,KAAK,EAAE,gDAAgD;QACvD,OAAO,EAAE,uCAAuC;QAChD,aAAa,EAAE,CAAC,2BAA2B,EAAE,eAAe,CAAC;KAC9D;IACD;QACE,EAAE,EAAE,6BAA6B;QACjC,KAAK,EAAE,6CAA6C;QACpD,OAAO,EAAE,yCAAyC;QAClD,aAAa,EAAE,CAAC,2BAA2B,EAAE,eAAe,CAAC;KAC9D;IACD;QACE,EAAE,EAAE,yBAAyB;QAC7B,KAAK,EAAE,kCAAkC;QACzC,OAAO,EAAE,qCAAqC;QAC9C,aAAa,EAAE,CAAC,yBAAyB,EAAE,eAAe,CAAC;KAC5D;IACD;QACE,EAAE,EAAE,kBAAkB;QACtB,KAAK,EAAE,uCAAuC;QAC9C,OAAO,EAAE,8BAA8B;QACvC,aAAa,EAAE,CAAC,kBAAkB,CAAC;QACnC,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,mBAAmB;QACvB,KAAK,EAAE,qCAAqC;QAC5C,OAAO,EAAE,4BAA4B;QACrC,aAAa,EAAE,CAAC,qBAAqB,CAAC;KACvC;CACF,CAAC;AAEF,MAAM,CAAC,KAAK,UAAU,YAAY;IAChC,MAAM,KAAK,GAA0B,EAAE,CAAC;IACxC,MAAM,IAAI,GAAG,WAAW,EAAE,CAAC;IAE3B,KAAK,MAAM,UAAU,IAAI,eAAe,EAAE,CAAC;QACzC,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;QAC3E,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;QACjG,MAAM,gBAAgB,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,QAAQ,KAAK,UAAU,CAAC,CAAC,MAAM,CAAC;QAErG,KAAK,CAAC,IAAI,CAAC;YACT,EAAE,EAAE,UAAU,CAAC,EAAE;YACjB,KAAK,EAAE,UAAU,CAAC,KAAK;YACvB,OAAO,EAAE,UAAU,CAAC,OAAO;YAC3B,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,QAAQ,EAAE,MAAM,CAAC,QAAQ,CAAC,MAAM;YAChC,gBAAgB;YAChB,aAAa;YACb,aAAa,EAAE,UAAU,CAAC,aAAa;YACvC,MAAM,EAAE,UAAU,CAAC,UAAU,EAAE,aAA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package/dist/src/demo.js

@@ -51,6 +51,12 @@ const DEMO_SCENARIOS = [
         fixture: "fixtures/codex-connector-auth-cache.md",
         description: "App connectors keep stale `link_*` auth or discovery metadata after reauth-required responses."
     },
+    {
+        id: "mcp-discovery-mismatch",
+        title: "Codex MCP discovery mismatch",
+        fixture: "fixtures/codex-mcp-discovery-mismatch.md",
+        description: "MCP servers work in CLI or one config scope but are absent in Desktop, VS Code, WSL, or project-local sessions."
+    },
     {
         id: "token-burn",
         title: "Codex token burn",
@@ -136,6 +142,7 @@ export function renderDemoMarkdown(result) {
         "trace-to-skill demo clipboard-attachment",
         "trace-to-skill demo deeplink-launch",
         "trace-to-skill demo connector-auth-cache",
+        "trace-to-skill demo mcp-discovery-mismatch",
         "trace-to-skill demo file-tree-ui",
         "trace-to-skill demo usage-reset-drift",
         "```",
@@ -162,6 +169,7 @@ export function renderDemoScenarioList(scenarios = listDemoScenarios()) {
         "trace-to-skill demo clipboard-attachment",
         "trace-to-skill demo deeplink-launch",
         "trace-to-skill demo connector-auth-cache",
+        "trace-to-skill demo mcp-discovery-mismatch",
         "trace-to-skill demo --list",
         "```",
         ""

package/dist/src/demo.js.map

@@ -1 +1 @@
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package/dist/src/rules.js

@@ -379,6 +379,29 @@ const RULES = [
         suggestedRule: "When Codex remote-control or mobile routing fails, capture desktop/app/CLI versions, mobile OS/app version, host id, remote-control status, listener pid/executable path, bound port, cache directory id, helper bundle completeness, active server_name/enrollment, workspace root, last mobile command id, and whether re-pairing or restarting the listener changes the route.",
         suggestedSkill: "codex-remote-control-triage"
     },
+    {
+        kind: "codex_mcp_discovery_mismatch",
+        severity: "high",
+        title: "Codex MCP discovery or config-scope mismatch",
+        why: "MCP servers can work in Codex CLI or one config scope while Desktop, VS Code, WSL, remote, or project-local sessions silently load another scope and expose no tools.",
+        patterns: [
+            /\bMCP servers? not detected\b.{0,220}\b(VS Code|extension|IDE|Desktop|Codex App)\b.{0,220}\b(working|works|detected|listed|available)\b.{0,120}\b(Codex CLI|CLI|\/mcp)\b/i,
+            /\b(Codex CLI|CLI|\/mcp|codex mcp list)\b.{0,220}\b(working|works|detects?|lists?|shows?|can access)\b.{0,220}\b(VS Code|extension|IDE|Desktop|Codex App)\b.{0,220}\b(no MCP|empty|not detected|missing|unknown MCP server|not exposed|not wired)\b/i,
+            /\b(VS Code|extension|IDE|Desktop|Codex App)\b.{0,220}\b(no MCP|list_mcp_resources remains empty|list_mcp_resource_templates.*empty|unknown MCP server|not detected|missing|not exposed|not registered)\b.{0,220}\b(Codex CLI|CLI|\/mcp|codex mcp list)\b.{0,220}\b(works|working|detects?|lists?|shows?)\b/i,
+            /\bproject[- ](?:scoped|level|local)\b.{0,160}\b\.codex\/config\.toml\b.{0,220}\b(ignored|not loaded|does not load|not picked up|does not pick up|absent|missing|unavailable)\b/i,
+            /\b\.codex\/config\.toml\b.{0,220}\b(project[- ](?:scoped|level|local)|trusted project|workspace)\b.{0,220}\b(ignored|not loaded|does not load|not picked up|does not pick up|absent|missing|unavailable)\b/i,
+            /\b(codex mcp get|codex mcp list)\b.{0,180}\b(No MCP server named|only shows servers from|does not show|absent|missing)\b.{0,180}\b(~\/\.codex\/config\.toml|\.codex\/config\.toml|project[- ](?:scoped|level|local)|global|user[- ]level)\b/i,
+            /\b(user[- ]level|global|~\/\.codex\/config\.toml)\b.{0,180}\b(works|detected|loads?)\b.{0,180}\b(project[- ](?:scoped|level|local)|\.codex\/config\.toml)\b.{0,180}\b(does not|doesn't|not|ignored|missing|unavailable)\b/i,
+            /\bmove(?:d)?\b.{0,160}\b(MCP server|same MCP|definition|config)\b.{0,120}\b(to|into)\b.{0,80}\b~\/\.codex\/config\.toml\b.{0,160}\b(works|detected|registered|fixes?|loads?)\b/i,
+            /\bCODEX_HOME\b.{0,220}\b(differs|different|not inherited|not set|VS Code|Desktop|WSL|remote|SSH|workspace|repo local)\b/i,
+            /\bWSL\b.{0,220}\b(config\.toml|CODEX_HOME|Windows-hosted|Windows `?config\.toml`?|\/home\/[^/\s]+\/\.codex\/config\.toml)\b.{0,220}\b(opens?|references?|uses?|points? to)\b.{0,120}\b(Windows|wrong|C:\\\\Users|not WSL)\b/i,
+            /\bOpen config\.toml in WSL environment\b.{0,220}\b(Windows|wrong config|C:\\\\Users|not WSL|still opens)\b/i,
+            /\b\.vscode[\\\/]mcp\.json\b.{0,220}\b(Codex|extension|IDE)\b.{0,220}\b(not supported|stopped recognizing|not detected|never supported|ignored)\b/i,
+            /\b(mcp__[-A-Za-z0-9_]+|mcp__\*)\b.{0,180}\b(not exposed|not wired|current session|old conversation|new conversation|curated namespaces only|missing)\b/i
+        ],
+        suggestedRule: "When reporting Codex MCP discovery or config-scope mismatches, capture app/CLI/extension version, OS, IDE, remote/WSL/SSH state, workspace root, effective CODEX_HOME, all config files considered (`~/.codex/config.toml`, project `.codex/config.toml`, `.vscode/mcp.json`, `.mcp.json`), exact MCP sections without secrets, trust/profile/default-permissions state, `codex mcp list` and `codex mcp get <server>`, CLI versus Desktop/VS Code comparison, loaded config path or extension logs, whether moving the same server to user-global config fixes it, whether reload/restart/new conversation changes tool exposure, and whether the current session exposes any `mcp__*` tools.",
+        suggestedSkill: "codex-mcp-discovery-triage"
+    },
     {
         kind: "codex_mcp_runtime",
         severity: "high",

package/dist/src/rules.js.map

@@ -1 +1 @@
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package/dist/src/types.d.ts

@@ -1,5 +1,5 @@
 export type Severity = "low" | "medium" | "high" | "critical";
-export type FindingKind = "premature_completion" | "tests_not_run" | "test_failure" | "ignored_instruction" | "hallucinated_file" | "over_editing" | "unsafe_command" | "secret_exposure" | "sensitive_file_access" | "hidden_unicode" | "prompt_injection" | "codex_remote_compact" | "context_compaction" | "codex_latest_turn_drift" | "codex_latency_regression" | "codex_thinking_hang" | "codex_clipboard_attachment" | "codex_deeplink_launch" | "codex_connector_auth_cache" | "codex_approval_friction" | "sandbox_permission" | "codex_windows_helper_path" | "codex_connectivity" | "codex_remote_control" | "codex_mcp_runtime" | "codex_plugin_runtime" | "codex_file_tree_ui" | "codex_session_state" | "codex_token_burn" | "codex_resource_leak" | "codex_tool_call_integrity" | "codex_usage_reset_drift" | "quota_mismatch" | "mcp_risk" | "weak_evidence";
+export type FindingKind = "premature_completion" | "tests_not_run" | "test_failure" | "ignored_instruction" | "hallucinated_file" | "over_editing" | "unsafe_command" | "secret_exposure" | "sensitive_file_access" | "hidden_unicode" | "prompt_injection" | "codex_remote_compact" | "context_compaction" | "codex_latest_turn_drift" | "codex_latency_regression" | "codex_thinking_hang" | "codex_clipboard_attachment" | "codex_deeplink_launch" | "codex_connector_auth_cache" | "codex_approval_friction" | "sandbox_permission" | "codex_windows_helper_path" | "codex_connectivity" | "codex_remote_control" | "codex_mcp_discovery_mismatch" | "codex_mcp_runtime" | "codex_plugin_runtime" | "codex_file_tree_ui" | "codex_session_state" | "codex_token_burn" | "codex_resource_leak" | "codex_tool_call_integrity" | "codex_usage_reset_drift" | "quota_mismatch" | "mcp_risk" | "weak_evidence";
 export interface TraceInput {
     path: string;
     content: string;

package/docs/BENCHMARK.md

@@ -26,6 +26,7 @@ This benchmark runs the public fixture pack that ships with the repository and p
 | MCP config with secret exposure | `fixtures/mcp-risk.json` | 59 | 2 | 1 | `mcp_risk`, `secret_exposure` | pass |
 | Sensitive file access in agent context | `fixtures/sensitive-file-access.md` | 75 | 2 | 0 | `sensitive_file_access`, `weak_evidence` | pass |
 | Codex MCP runtime failure | `fixtures/codex-mcp-runtime.md` | 75 | 2 | 0 | `codex_mcp_runtime`, `weak_evidence` | pass |
+| Codex MCP discovery and config-scope mismatch | `fixtures/codex-mcp-discovery-mismatch.md` | 75 | 2 | 0 | `codex_mcp_discovery_mismatch`, `weak_evidence` | pass |
 | Codex plugin runtime and bundled capability failure | `fixtures/codex-plugin-runtime.md` | 59 | 3 | 0 | `codex_plugin_runtime`, `codex_windows_helper_path`, `weak_evidence` | pass |
 | Codex file tree and workspace navigation UI failure | `fixtures/codex-file-tree-ui.md` | 75 | 2 | 0 | `codex_file_tree_ui`, `weak_evidence` | pass |
 | Codex session resume and state failure | `fixtures/codex-session-state.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_session_state`, `weak_evidence` | pass |

package/docs/CODEX_ISSUE_MAP.md

@@ -30,6 +30,7 @@ npx trace-to-skill diagnostics-bundle ~/.codex --output codex-diagnostics
 | Clipboard, paste, and generated attachment regressions | `Copy as Markdown` missing, Copy menu only exports metadata, long pasted prompts become `Pasted text.txt`, generated attachments cannot preview/edit/revert, `/goal` ignores non-empty fileAttachments | `codex_clipboard_attachment` | `trace-to-skill codex-report ./runs` or `trace-to-skill demo clipboard-attachment` |
 | Deeplink, OAuth callback, and external launch regressions | `codex://oauth_callback?code=...` fails, `Unable to find Electron app`, `app\oauth_callback?code=...`, notification `type=click&tag=...` becomes an app path, AppX/MSIX protocol evidence, `codex app .` only focuses | `codex_deeplink_launch` | `trace-to-skill codex-report ./runs` or `trace-to-skill demo deeplink-launch` |
 | App connector auth cache and stale link regressions | `401 Reauthentication required`, `refresh token was revoked`, stale `link_*`, `isAccessible: false`, `codex_apps_tools` or `codex_app_directory` cache regeneration keeps broken connector state | `codex_connector_auth_cache` | `trace-to-skill codex-report ./runs` or `trace-to-skill demo connector-auth-cache` |
+| MCP discovery and config-scope mismatches | CLI `/mcp` works but VS Code/Desktop has no `mcp__*` tools, project `.codex/config.toml` ignored, `codex mcp get` says `No MCP server named`, WSL opens Windows `config.toml`, `CODEX_HOME` differs | `codex_mcp_discovery_mismatch` | `trace-to-skill codex-report ./runs` or `trace-to-skill demo mcp-discovery-mismatch` |
 | Approval persistence and MCP approval friction | `Approve for this session` is not remembered, command approval cache misses, repeated file-change approvals, `approval_policy = "never"` still prompts for MCP tools, per-tool approval configs explode | `codex_approval_friction` | `trace-to-skill codex-report ./runs` |
 | Config and Preferences drift | legacy `profile` / `[profiles.*]`, `configVersionConflict`, Preferences `Unable to save`, stale model pin, missing `default_permissions` profile, enabled plugin cache missing, Windows elevated sandbox mode | `sandbox_permission`, `codex_plugin_runtime`, `codex_approval_friction` | `trace-to-skill config-audit ~/.codex --format json` |
 | Bundled plugin cache and marketplace drift | Computer Use unavailable, Browser/Chrome plugin unavailable, generated runtime marketplace omits bundled plugins, missing `.mcp.json` or `plugin.json`, helper app not installed, `CODEX_HOME` points at another runtime | `codex_plugin_runtime`, `codex_mcp_runtime` | `trace-to-skill plugin-audit ~/.codex --app /Applications/Codex.app --format json` |
@@ -66,6 +67,7 @@ npx trace-to-skill diagnostics-bundle ~/.codex --output codex-diagnostics
 - Include exact Copy menu items, paste source size, generated attachment name/path/size, visible editor text, `pasted-text-attachments.json` or fileAttachments metadata, `/goal` or submit path, preview/edit/revert actions, and clipboard payload format for clipboard/attachment regressions.
 - Include exact redacted `codex://` URI shape, connector/plugin, browser, error dialog text, app running state, AppX/MSIX protocol registration evidence such as AppUserModelID and DelegateExecute, HKCU/HKCR `codex` keys, command-line arguments, `Start-Process "codex://test"` repro, and repair/reinstall/re-register attempts for deeplink/OAuth launch regressions.
 - Include connector/plugin name and id, installed plugin root, exact Codex Apps tool name, 401/reauth text, `link_*` id before and after reconnect/cache regeneration, `isAccessible` state, redacted `codex_apps_tools`/`codex_app_directory` metadata, ChatGPT app page state, and external MCP workaround result for connector auth-cache regressions.
+- Include effective `CODEX_HOME`, config files considered, redacted MCP sections, trust/profile/default-permissions state, `codex mcp list/get`, CLI-versus-Desktop/VS Code comparison, loaded config path/log lines, WSL/remote/SSH state, and restart/reload/new-conversation results for MCP discovery mismatches.
 - Include selected approval scope, displayed vs executed command, MCP server/tool names, visible args, repeated prompt count, and config snippets for approval-friction reports.
 - Include `config-audit` output for Preferences/config, sandbox, model-pin, MCP approval, and plugin-cache reports.
 - Include `plugin-audit` output, plugin name/version, cache path, helper path, manifest path, runtime marketplace, app-bundle marketplace, native pipe env vars, settings/plugin-list errors, and restart behavior for plugin runtime failures.
@@ -86,6 +88,7 @@ npx trace-to-skill diagnostics-bundle ~/.codex --output codex-diagnostics
 - Latency regressions: https://github.com/openai/codex/issues/24422, https://github.com/openai/codex/issues/21527, https://github.com/openai/codex/issues/11984, https://github.com/openai/codex/issues/12161
 - Deeplink, OAuth callback, and external launch regressions: https://github.com/openai/codex/issues/25203, https://github.com/openai/codex/issues/25231, https://github.com/openai/codex/issues/25368, https://github.com/openai/codex/issues/25333
 - App connector auth cache and stale link regressions: https://github.com/openai/codex/issues/24675, https://github.com/openai/codex/issues/25443
+- MCP discovery and config-scope mismatches: https://github.com/openai/codex/issues/6465, https://github.com/openai/codex/issues/13025, https://github.com/openai/codex/issues/13549
 - Approval persistence and MCP approval friction: https://github.com/openai/codex/issues/4212, https://github.com/openai/codex/issues/13476, https://github.com/openai/codex/issues/2998
 - Config and Preferences drift: https://github.com/openai/codex/issues/25440, https://github.com/openai/codex/issues/25442, https://github.com/openai/codex/issues/20538, https://github.com/openai/codex/issues/24963
 - Latest-turn drift and compaction memory loss: https://github.com/openai/codex/issues/8648, https://github.com/openai/codex/issues/5957, https://github.com/openai/codex/issues/10823, https://github.com/openai/codex/issues/11626

package/docs/DEMO.md

@@ -1,10 +1,10 @@
 # trace-to-skill Demo
 
-Scenario: **Codex app connector auth cache regression**
+Scenario: **Codex MCP discovery mismatch**
 
-App connectors keep stale `link_*` auth or discovery metadata after reauth-required responses.
+MCP servers work in CLI or one config scope but are absent in Desktop, VS Code, WSL, or project-local sessions.
 
-Fixture: `fixtures/codex-connector-auth-cache.md`
+Fixture: `fixtures/codex-mcp-discovery-mismatch.md`
 
 This is a packaged public fixture, so you can try the project without collecting a private trace first.
 
@@ -14,7 +14,7 @@ This is a packaged public fixture, so you can try the project without collecting
 
 Score: **75/100**
 
-Likely failure class: **Codex app connector auth cache or stale link regression (codex_connector_auth_cache, high)**
+Likely failure class: **Codex MCP discovery or config-scope mismatch (codex_mcp_discovery_mismatch, high)**
 
 Agent workflow needs clearer verification, instruction, or security hardening before broad reuse.
 
@@ -23,25 +23,22 @@ Agent workflow needs clearer verification, instruction, or security hardening be
 ```md
 ### What happened?
 
-trace-to-skill detected Codex app connector auth cache or stale link regression (codex_connector_auth_cache). Codex app connectors can keep stale server-side or local `link_*` authorization metadata after reauth-required responses, making plugin reinstall and app restart look successful while connector tools still fail.
+trace-to-skill detected Codex MCP discovery or config-scope mismatch (codex_mcp_discovery_mismatch). MCP servers can work in Codex CLI or one config scope while Desktop, VS Code, WSL, remote, or project-local sessions silently load another scope and expose no tools.
 
 ### Detected failure class
 
-- codex_connector_auth_cache: Codex app connector auth cache or stale link regression (high)
+- codex_mcp_discovery_mismatch: Codex MCP discovery or config-scope mismatch (high)
 
 ### Evidence
 
-#### Codex app connector auth cache or stale link regression
-- fixtures/codex-connector-auth-cache.md:13 - - A read-only Linear tool is visible, but `mcp__codex_apps__linear._list_teams` returns `401: "Server returned 401: 'Reauthentication required'"`.
-- fixtures/codex-connector-auth-cache.md:14 - - Codex Desktop also showed `Your access token could not be refreshed because your refresh token was revoked. Please log out and sign in again` during an active session.
-- fixtures/codex-connector-auth-cache.md:15 - - Restarting Codex Desktop did not fix the connector.
-- fixtures/codex-connector-auth-cache.md:16 - - `codex plugin remove linear@openai-curated` followed by `codex plugin add linear@openai-curated` did not fix auth.
-- fixtures/codex-connector-auth-cache.md:17 - - Moving aside `~/.codex/cache/codex_apps_tools/*.json` and `~/.codex/cache/codex_app_directory/*.json` regenerated files but kept the same connector link id.
-- fixtures/codex-connector-auth-cache.md:18 - - Before and after cache regeneration, Linear still referenced `link_69ebf2fff8cc8191a42ae4b585c191f6`.
+#### Codex MCP discovery or config-scope mismatch
+- fixtures/codex-mcp-discovery-mismatch.md:20 - MCP servers not detected in Codex VS Code extension, but working in Codex CLI.
+- fixtures/codex-mcp-discovery-mismatch.md:60 - Open config.toml in WSL environment still opens the Windows config.toml.
+- fixtures/codex-mcp-discovery-mismatch.md:63 - CODEX_HOME differs between CLI, VS Code, WSL, remote SSH, and the standalone app.
 
 ### Diagnostics to attach
 
-- When reporting Codex app connector auth-cache regressions, capture app/CLI version, OS, connector/plugin name and id, installed plugin root, exact tool name such as `mcp__codex_apps__linear.*`, error text, `link_*` id before and after reconnect, `isAccessible` state, relevant `~/.codex/cache/codex_apps_tools` and `codex_app_directory` metadata without tokens, restart/remove/re-add/cache-clear attempts, whether the ChatGPT app page shows Connect, whether a server-side link appears unchanged, and whether an external MCP workaround succeeds.
+- When reporting Codex MCP discovery or config-scope mismatches, capture app/CLI/extension version, OS, IDE, remote/WSL/SSH state, workspace root, effective CODEX_HOME, all config files considered (`~/.codex/config.toml`, project `.codex/config.toml`, `.vscode/mcp.json`, `.mcp.json`), exact MCP sections without secrets, trust/profile/default-permissions state, `codex mcp list` and `codex mcp get <server>`, CLI versus Desktop/VS Code comparison, loaded config path or extension logs, whether moving the same server to user-global config fixes it, whether reload/restart/new conversation changes tool exposure, and whether the current session exposes any `mcp__*` tools.
 
 ### Privacy
 
@@ -50,25 +47,20 @@ trace-to-skill detected Codex app connector auth cache or stale link regression
 
 ## Findings
 
-### 1. Codex app connector auth cache or stale link regression
+### 1. Codex MCP discovery or config-scope mismatch
 
 Severity: **high**
 
-Codex app connectors can keep stale server-side or local `link_*` authorization metadata after reauth-required responses, making plugin reinstall and app restart look successful while connector tools still fail.
+MCP servers can work in Codex CLI or one config scope while Desktop, VS Code, WSL, remote, or project-local sessions silently load another scope and expose no tools.
 
 Evidence:
-- `fixtures/codex-connector-auth-cache.md:13` - A read-only Linear tool is visible, but `mcp__codex_apps__linear._list_teams` returns `401: "Server returned 401: 'Reauthentication required'"`.
-- `fixtures/codex-connector-auth-cache.md:14` - Codex Desktop also showed `Your access token could not be refreshed because your refresh token was revoked. Please log out and sign in again` during an active session.
-- `fixtures/codex-connector-auth-cache.md:15` - Restarting Codex Desktop did not fix the connector.
-- `fixtures/codex-connector-auth-cache.md:16` - `codex plugin remove linear@openai-curated` followed by `codex plugin add linear@openai-curated` did not fix auth.
-- `fixtures/codex-connector-auth-cache.md:17` - Moving aside `~/.codex/cache/codex_apps_tools/*.json` and `~/.codex/cache/codex_app_directory/*.json` regenerated files but kept the same connector link id.
-- `fixtures/codex-connector-auth-cache.md:18` - Before and after cache regeneration, Linear still referenced `link_69ebf2fff8cc8191a42ae4b585c191f6`.
-- `fixtures/codex-connector-auth-cache.md:19` - The regenerated app directory still reported `isAccessible: false`.
-- `fixtures/codex-connector-auth-cache.md:21` - An external Linear MCP workaround succeeded with `codex mcp add linear --url https://mcp.linear.app/mcp`:
+- `fixtures/codex-mcp-discovery-mismatch.md:20` MCP servers not detected in Codex VS Code extension, but working in Codex CLI.
+- `fixtures/codex-mcp-discovery-mismatch.md:60` Open config.toml in WSL environment still opens the Windows config.toml.
+- `fixtures/codex-mcp-discovery-mismatch.md:63` CODEX_HOME differs between CLI, VS Code, WSL, remote SSH, and the standalone app.
 
 Suggested rule:
 
-> When reporting Codex app connector auth-cache regressions, capture app/CLI version, OS, connector/plugin name and id, installed plugin root, exact tool name such as `mcp__codex_apps__linear.*`, error text, `link_*` id before and after reconnect, `isAccessible` state, relevant `~/.codex/cache/codex_apps_tools` and `codex_app_directory` metadata without tokens, restart/remove/re-add/cache-clear attempts, whether the ChatGPT app page shows Connect, whether a server-side link appears unchanged, and whether an external MCP workaround succeeds.
+> When reporting Codex MCP discovery or config-scope mismatches, capture app/CLI/extension version, OS, IDE, remote/WSL/SSH state, workspace root, effective CODEX_HOME, all config files considered (`~/.codex/config.toml`, project `.codex/config.toml`, `.vscode/mcp.json`, `.mcp.json`), exact MCP sections without secrets, trust/profile/default-permissions state, `codex mcp list` and `codex mcp get <server>`, CLI versus Desktop/VS Code comparison, loaded config path or extension logs, whether moving the same server to user-global config fixes it, whether reload/restart/new conversation changes tool exposure, and whether the current session exposes any `mcp__*` tools.
 
 
 ## Reporter Notes
@@ -88,6 +80,7 @@ Suggested rule:
 - `thinking-hang`: A turn or tool call completes, but the session stays on Thinking or Working with no streamed follow-up.
 - `clipboard-attachment`: Copy as Markdown, long-paste conversion, or generated Pasted text.txt attachments break prompt and report workflows.
 - `deeplink-launch`: OAuth callbacks, notification clicks, mobile links, or `codex app <path>` external activation fail to route into Codex.
+- `connector-auth-cache`: App connectors keep stale `link_*` auth or discovery metadata after reauth-required responses.
 - `token-burn`: Usage drains from background polling, idle activity, compaction loops, retries, or cached-heavy turns.
 - `patch-overwrite`: `apply_patch` accepts `*** Add File` for an existing path, turning a create operation into a silent overwrite.
 - `sensitive-files`: Secrets, local credentials, production env files, or private databases enter agent context.
@@ -104,6 +97,7 @@ trace-to-skill demo thinking-hang
 trace-to-skill demo clipboard-attachment
 trace-to-skill demo deeplink-launch
 trace-to-skill demo connector-auth-cache
+trace-to-skill demo mcp-discovery-mismatch
 trace-to-skill demo file-tree-ui
 trace-to-skill demo usage-reset-drift
 ```

package/docs/DISCOVERY.md

@@ -27,6 +27,7 @@ This page is written for maintainers, search engines, package indexes, and AI re
 - Codex login or response streaming fails because of `token_exchange_failed`, `auth.openai.com/oauth/token`, missing CA certificates, proxy/MITM, IPv6 fallback, Cloudflare challenge, or `stream disconnected before completion`.
 - Codex mobile or remote-control appears connected but routes through stale listeners, stale enrollment, incomplete helper bundles, empty backend environments, or stale Android/iOS session state.
 - Codex MCP tools are visible in `tools/list` but fail at runtime because approval is cancelled, elicitation is unsupported in exec mode, namespace or `serverName` metadata is dropped, routed names become `unsupported call`, or stdio transport closes.
+- Codex MCP servers work in CLI or one config scope but are absent in VS Code, Desktop, WSL, remote, project-local, or older-conversation sessions because the effective config path, `CODEX_HOME`, trust/profile state, or tool exposure differs.
 - Codex approval flow repeatedly prompts after `Approve for this session`, forgets a safe approval scope, or forces large trusted MCP servers into noisy per-tool approval configs.
 - Codex config drift makes Preferences unable to save, keeps legacy `profile` / `[profiles.*]` config after migration, pins an unavailable model, points `default_permissions` at a missing profile, enables Windows elevated sandbox mode, or references plugin cache entries that are missing on disk.
 - Codex Desktop file tree, folder icon, floating file panel, or built-in file preview disappears, goes stale, or cannot be revealed by `View > Toggle File Tree`.
@@ -67,6 +68,7 @@ npx trace-to-skill demo thinking-hang
 npx trace-to-skill demo clipboard-attachment
 npx trace-to-skill demo deeplink-launch
 npx trace-to-skill demo connector-auth-cache
+npx trace-to-skill demo mcp-discovery-mismatch
 npx trace-to-skill scorecard .
 npx trace-to-skill lint-agents .
 npx trace-to-skill guard-github-event "$GITHUB_EVENT_PATH"

package/docs/FAILURE_TAXONOMY.md

@@ -104,6 +104,14 @@ Common signals include `user cancelled MCP tool call`, `request_user_input is no
 
 The fix is to capture the Codex version, MCP server name and transport, tool name, exposed callable name, whether `tools/list` and manual `tools/call` succeed, `approval_policy`, sandbox mode, exec or interactive mode, elicitation setting, namespace or `serverName` metadata, exact `item.started` / `item.completed` JSONL, stderr or backpressure evidence, and whether restarting or reinitializing the transport changes the result.
 
+## Codex MCP Discovery Mismatch
+
+Codex MCP servers can work in CLI or one config scope but disappear in another surface before any tool call is possible. This is different from runtime failure: the user may have no `mcp__*` tools exposed in VS Code, Desktop, WSL, a remote session, project-local `.codex/config.toml`, or an older conversation even though CLI `/mcp` works.
+
+Common signals include `MCP servers not detected in Codex VS Code extension (but working in Codex CLI)`, `list_mcp_resources remains empty`, `unknown MCP server`, project `.codex/config.toml` ignored while `~/.codex/config.toml` works, `codex mcp get <server>` returning `No MCP server named`, WSL opening a Windows-hosted `config.toml`, `CODEX_HOME` mismatch, `.vscode/mcp.json` confusion, curated namespaces only, or a new conversation seeing tools while the previous conversation does not.
+
+The fix is to capture app/CLI/extension version, OS, IDE, remote/WSL/SSH state, workspace root, effective `CODEX_HOME`, config files considered, redacted MCP sections, trust/profile/default-permissions state, `codex mcp list`, `codex mcp get <server>`, CLI-versus-Desktop/VS Code comparison, loaded config path or extension logs, whether moving the same server to user-global config fixes it, and restart/reload/new-conversation behavior.
+
 ## Codex Plugin Runtime
 
 Codex Desktop can show a plugin, connector, Browser, Computer Use, or bundled skill as available while the shared plugin runtime is not actually usable. Common causes include missing native pipe/helper metadata, plugin-list schema drift, stale plugin cache reconciliation, file-lock issues, or installed plugins being silently downgraded.

package/docs/OPENAI_OSS_BRIEF.md

@@ -3,18 +3,18 @@
 | Field | Value |
 | --- | --- |
 | Repository | https://github.com/grnbtqdbyx-create/trace-to-skill |
-| Package | trace-to-skill@0.1.63 |
+| Package | trace-to-skill@0.1.64 |
 | License | Apache-2.0 |
 | Codex readiness | ready (100/100) |
-| Benchmark | pass, 30 cases |
+| Benchmark | pass, 31 cases |
 
 ## Why This Repository Qualifies
 
-trace-to-skill helps open-source maintainers adopt Codex safely by turning failed coding-agent runs into evidence-backed rules, reusable workflows, and CI gates. It supports real maintenance work: PR review, issue triage, release quality, MCP risk, prompt-injection defense, privacy-preserving trace sharing, and repeat failure reduction. The repository is ready, scores 100/100 on the local Codex readiness doctor, and ships a deterministic benchmark with 30 public fixture cases.
+trace-to-skill helps open-source maintainers adopt Codex safely by turning failed coding-agent runs into evidence-backed rules, reusable workflows, and CI gates. It supports real maintenance work: PR review, issue triage, release quality, MCP risk, prompt-injection defense, privacy-preserving trace sharing, and repeat failure reduction. The repository is ready, scores 100/100 on the local Codex readiness doctor, and ships a deterministic benchmark with 31 public fixture cases.
 
 ### 500-Character Version
 
-> trace-to-skill helps open-source maintainers adopt Codex safely by turning failed coding-agent runs into evidence-backed rules, reusable workflows, and CI gates. It supports real maintenance work: PR review, issue triage, release quality, MCP risk, prompt-injection defense, privacy-preserving trace sharing, and repeat failure reduction. The repository is ready, scores 100/100 on the local Codex readiness doctor, and ships a deterministic benchmark with 30 public fixture cases.
+> trace-to-skill helps open-source maintainers adopt Codex safely by turning failed coding-agent runs into evidence-backed rules, reusable workflows, and CI gates. It supports real maintenance work: PR review, issue triage, release quality, MCP risk, prompt-injection defense, privacy-preserving trace sharing, and repeat failure reduction. The repository is ready, scores 100/100 on the local Codex readiness doctor, and ships a deterministic benchmark with 31 public fixture cases.
 
 ## How API Credits Would Be Used
 
@@ -27,10 +27,10 @@ API credits would power optional maintainer workflows on top of the local determ
 ## Evidence
 
 - Public repository: https://github.com/grnbtqdbyx-create/trace-to-skill
-- One-command package: npx trace-to-skill@0.1.63
+- One-command package: npx trace-to-skill@0.1.64
 - Open-source license: Apache-2.0
 - Codex readiness doctor: ready, 100/100, 0 failed checks.
-- Public fixture benchmark: pass, 30 cases.
+- Public fixture benchmark: pass, 31 cases.
 - Maintainer control: generated rules are suggestions, evidence is line-linked, and secrets can be redacted before sharing.
 
 ## Next Steps Before Submitting

package/docs/SCORECARD.md

@@ -9,7 +9,7 @@ Status: **pass**
 | Failed doctor checks | 0 |
 | Critical findings | 0 |
 | Built-in benchmark | pass |
-| Benchmark cases | 30 |
+| Benchmark cases | 31 |
 
 ## Doctor Summary
 
@@ -43,6 +43,7 @@ This benchmark runs the public fixture pack that ships with the repository and p
 | MCP config with secret exposure | `fixtures/mcp-risk.json` | 59 | 2 | 1 | `mcp_risk`, `secret_exposure` | pass |
 | Sensitive file access in agent context | `fixtures/sensitive-file-access.md` | 75 | 2 | 0 | `sensitive_file_access`, `weak_evidence` | pass |
 | Codex MCP runtime failure | `fixtures/codex-mcp-runtime.md` | 75 | 2 | 0 | `codex_mcp_runtime`, `weak_evidence` | pass |
+| Codex MCP discovery and config-scope mismatch | `fixtures/codex-mcp-discovery-mismatch.md` | 75 | 2 | 0 | `codex_mcp_discovery_mismatch`, `weak_evidence` | pass |
 | Codex plugin runtime and bundled capability failure | `fixtures/codex-plugin-runtime.md` | 59 | 3 | 0 | `codex_plugin_runtime`, `codex_windows_helper_path`, `weak_evidence` | pass |
 | Codex file tree and workspace navigation UI failure | `fixtures/codex-file-tree-ui.md` | 75 | 2 | 0 | `codex_file_tree_ui`, `weak_evidence` | pass |
 | Codex session resume and state failure | `fixtures/codex-session-state.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_session_state`, `weak_evidence` | pass |

package/docs/USE_CASES.md

@@ -17,13 +17,14 @@ npx trace-to-skill demo thinking-hang
 npx trace-to-skill demo clipboard-attachment
 npx trace-to-skill demo deeplink-launch
 npx trace-to-skill demo connector-auth-cache
+npx trace-to-skill demo mcp-discovery-mismatch
 ```
 
 What it proves:
 
 - packaged fixtures can produce a real Codex issue report immediately
 - maintainers can inspect the output shape before sharing any private log
-- demos cover remote compact failures, Windows helper path failures, patch overwrite safety, approval friction, latency, Thinking hangs, clipboard/attachment regressions, deeplink/OAuth launch regressions, connector auth-cache regressions, token burn, sensitive files, and prompt injection
+- demos cover remote compact failures, Windows helper path failures, patch overwrite safety, approval friction, latency, Thinking hangs, clipboard/attachment regressions, deeplink/OAuth launch regressions, connector auth-cache regressions, MCP discovery/config-scope mismatches, token burn, sensitive files, and prompt injection
 
 See the generated demo output in [docs/DEMO.md](DEMO.md).
 
@@ -46,7 +47,7 @@ What it proves:
 Recommended CI surface:
 
 ```yaml
-- uses: grnbtqdbyx-create/trace-to-skill@v0.1.63
+- uses: grnbtqdbyx-create/trace-to-skill@v0.1.64
   with:
     mode: all
     doctor-threshold: "85"
@@ -286,7 +287,21 @@ This catches signals such as `401: "Server returned 401: 'Reauthentication requi
 
 Include app/CLI version, OS, connector/plugin name and id, installed plugin root, exact tool name, redacted `codex_apps_tools` and `codex_app_directory` metadata, `link_*` id before/after reconnect, `isAccessible` state, restart/remove/re-add/cache-clear/sign-in attempts, ChatGPT app page state, and whether an external MCP workaround succeeds.
 
-## 20. Patch Overwrite Guard
+## 20. Codex MCP Discovery And Config Scope Evidence
+
+Use this when MCP servers work in Codex CLI or one config scope but are missing in VS Code, Desktop, WSL, remote sessions, project-local config, or an older conversation.
+
+```bash
+npx trace-to-skill demo mcp-discovery-mismatch
+npx trace-to-skill analyze ./runs --format json
+npx trace-to-skill codex-report ./runs --output openai-codex-mcp-discovery.md
+```
+
+This catches signals such as `MCP servers not detected in Codex VS Code extension (but working in Codex CLI)`, `list_mcp_resources remains empty`, missing `mcp__*` tools, project `.codex/config.toml` ignored while `~/.codex/config.toml` works, `codex mcp get <server>` returning `No MCP server named`, WSL opening the Windows-hosted `config.toml`, `CODEX_HOME` mismatch, and tool exposure changing after restart, reload, or new conversation.
+
+Include app/CLI/extension version, OS, IDE, remote/WSL/SSH state, workspace root, effective `CODEX_HOME`, all config files considered (`~/.codex/config.toml`, project `.codex/config.toml`, `.vscode/mcp.json`, `.mcp.json`), redacted MCP sections, trust/profile/default-permissions state, `codex mcp list`, `codex mcp get <server>`, CLI-versus-Desktop/VS Code comparison, loaded config path/log lines, whether moving the same server to user-global config fixes it, and whether the current session exposes `mcp__*` tools.
+
+## 21. Patch Overwrite Guard
 
 Use this before applying a generated patch when you want create/update/delete semantics checked against the actual workspace.
 
@@ -303,7 +318,7 @@ For a public demo report:
 npx trace-to-skill demo patch-overwrite
 ```
 
-## 21. OpenAI Codex Issue Report
+## 22. OpenAI Codex Issue Report
 
 Use this when you want to file or update an OpenAI/Codex issue with a concise, evidence-backed report instead of pasting a full transcript.
 
@@ -316,7 +331,7 @@ The report includes the likely Codex failure class, line-linked evidence, diagno
 
 For a cluster-to-command map of current Codex issue patterns, see [CODEX_ISSUE_MAP.md](CODEX_ISSUE_MAP.md).
 
-## 22. Sensitive File Access Evidence
+## 23. Sensitive File Access Evidence
 
 Use this when a trace suggests an agent read, attached, uploaded, diffed, or indexed credential-bearing files.
 
@@ -329,7 +344,7 @@ This catches signals such as `.env`, `.env.production`, `.npmrc`, `.pypirc`, `.n
 
 Before publishing evidence, run `trace-to-skill redact` and attach only redacted excerpts plus the file path/class.
 
-## 23. GitHub Context Guard
+## 24. GitHub Context Guard
 
 Use this before an agent reads untrusted GitHub text.
 
@@ -346,7 +361,7 @@ Use it when:
 - a bot asks Codex to triage untrusted user reports
 - logs or comments might contain instructions like "ignore previous instructions" or "print secrets"
 
-## 24. Failed Agent Run To Reviewable Rule
+## 25. Failed Agent Run To Reviewable Rule
 
 Use this when a coding agent made a repeated workflow mistake.
 
@@ -364,7 +379,7 @@ Recommended maintainer loop:
 4. Copy only evidence-backed rules into the real policy file.
 5. Run `eval` or `scorecard` in CI so the same failure does not silently return.
 
-## 25. Privacy-Preserving Adoption
+## 26. Privacy-Preserving Adoption
 
 Use this when you want public evidence without leaking private traces.
 

package/fixtures/codex-mcp-discovery-mismatch.md

@@ -0,0 +1,75 @@
+# Codex MCP discovery mismatch fixture
+
+This fixture uses public, token-free examples of MCP servers being visible in one Codex surface or config scope but absent from another.
+
+## CLI works, VS Code extension has no tools
+
+Environment:
+
+- Codex CLI v0.58.0
+- Codex VS Code extension v0.4.40
+- macOS and Windows reports
+- MCP server defined in `~/.codex/config.toml`
+
+Observed behavior:
+
+```text
+Codex CLI /mcp shows playwright and supabase; tools are listed and callable.
+Codex VS Code extension says list_mcp_resources remains empty.
+The extension has no mcp__ prefixed tools exposed in this session.
+MCP servers not detected in Codex VS Code extension, but working in Codex CLI.
+```
+
+Another report:
+
+```text
+codex mcp list shows nxmcp in the terminal session.
+The Codex extension does not see Nx MCP tools in the current session tool list.
+CLI can access the MCP server and list tables, while the extension reports:
+resources/list failed: unknown MCP server 'postgres'
+```
+
+## Project config works in CLI but not Desktop
+
+A trusted project contains only a project-local MCP entry:
+
+```toml
+[mcp_servers.serena]
+command = "uvx"
+args = ["--from", "git+https://github.com/oraios/serena", "serena", "start-mcp-server", "--context", "codex", "--project-from-cwd"]
+```
+
+Observed behavior:
+
+```text
+Project-scoped .codex/config.toml is ignored for this thread/workspace.
+available MCP resources/templates are empty for Serena tools.
+codex mcp list only shows servers from ~/.codex/config.toml.
+codex mcp get serena returns: No MCP server named 'serena' found.
+User-level MCP config works in Codex CLI, Codex Desktop, and the Codex Cursor extension.
+Project-level MCP config works in Codex CLI only.
+If I move the exact same MCP server definition into ~/.codex/config.toml and restart Codex Desktop, it is detected and works normally.
+```
+
+## WSL opens the wrong config
+
+Windows app configuration:
+
+```text
+Agent environment and integrated terminal shell are set to WSL.
+Open config.toml in WSL environment still opens the Windows config.toml.
+Expected: /home/user/.codex/config.toml
+Actual: C:\Users\user\.codex\config.toml
+CODEX_HOME differs between CLI, VS Code, WSL, remote SSH, and the standalone app.
+```
+
+## Session exposure drift
+
+```text
+The standalone CLI /mcp can show tools while the VS Code assistant only exposes curated namespaces.
+If I start a new conversation in the VS Code extension, it sees the right MCP servers/functions.
+Switching back to the previous conversation loses them again.
+The current session exposes no mcp__* tools.
+```
+
+The report should include app/CLI/extension versions, OS, IDE, remote/WSL/SSH state, workspace root, effective `CODEX_HOME`, config files considered (`~/.codex/config.toml`, project `.codex/config.toml`, and IDE-level MCP config), redacted MCP sections, trust/profile/default-permissions state, `codex mcp list`, `codex mcp get <server>`, CLI-versus-Desktop/VS Code comparison, loaded config path or extension logs, whether moving the same server to global config fixes it, whether reload/restart/new conversation changes tool exposure, and whether the session exposes `mcp__*` tools.

package/llms.txt

@@ -23,6 +23,7 @@ Runtime: Node.js 20+
 - Codex auth and connectivity failures such as `token_exchange_failed`, `auth.openai.com/oauth/token`, missing `ca-certificates`, proxy or MITM TLS behavior, IPv6 fallback problems, Cloudflare challenge responses, and ChatGPT stream disconnects
 - Codex mobile and remote-control route health failures such as `Waiting for desktop`, `Directory Unavailable`, stale listeners on `127.0.0.1:14567`, stale `server_name` enrollment, empty backend environments, and incomplete helper bundles
 - Codex MCP runtime failures such as cancelled non-interactive approvals, `request_user_input is not supported in exec mode`, dropped namespace or `serverName` metadata, `unsupported call: mcp__...__...`, and closed `StdioServerTransport` sessions
+- Codex MCP discovery and config-scope mismatches where CLI `/mcp` works but VS Code, Desktop, WSL, project `.codex/config.toml`, `CODEX_HOME`, or an older conversation exposes no `mcp__*` tools
 - Codex resume and session-state failures such as frozen resume pickers, large rollout JSONL histories, short `session_index.jsonl`, sluggish Desktop thread rendering, dropped recent context after resume, archived chat loading failures, and `state_5.sqlite` / `goals_1.sqlite` migration drift
 - Codex file tree and workspace navigation UI failures such as `View > Toggle File Tree` doing nothing, missing folder icons, stale floating file panels, and built-in preview failures
 - Codex Thinking or Working hangs after accepted turns, successful local tools, or open Responses streams with no streamed assistant follow-up
@@ -72,6 +73,7 @@ npx trace-to-skill demo thinking-hang
 npx trace-to-skill demo clipboard-attachment
 npx trace-to-skill demo deeplink-launch
 npx trace-to-skill demo connector-auth-cache
+npx trace-to-skill demo mcp-discovery-mismatch
 npx trace-to-skill lint-agents .
 npx trace-to-skill guard-github-event "$GITHUB_EVENT_PATH"
 npx trace-to-skill guard-patch ./change.patch --root .
@@ -93,7 +95,7 @@ npx trace-to-skill init --comment --sarif
 ## GitHub Action
 
 ```yaml
-- uses: grnbtqdbyx-create/trace-to-skill@v0.1.63
+- uses: grnbtqdbyx-create/trace-to-skill@v0.1.64
   with:
     mode: all
     doctor-threshold: "85"
@@ -156,6 +158,9 @@ npx trace-to-skill init --comment --sarif
 - Codex mobile Waiting for desktop Directory Unavailable
 - Codex MCP unsupported call mcp__node_repl__js
 - Codex MCP tools/list succeeds but runtime call fails
+- Codex MCP servers not detected in VS Code extension but working in CLI
+- Codex project .codex/config.toml MCP ignored Desktop
+- Codex WSL opens Windows config.toml CODEX_HOME mismatch
 - Codex MCP Transport closed StdioServerTransport
 - Codex View Toggle File Tree does nothing
 - Codex missing file tree folder icon

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "trace-to-skill",
-  "version": "0.1.63",
+  "version": "0.1.64",
   "description": "Turn failed AI coding-agent runs into reusable AGENTS.md rules, SKILL.md files, and eval evidence.",
   "type": "module",
   "main": "dist/src/index.js",
@@ -104,6 +104,9 @@
     "codex-remote-control",
     "codex-mobile",
     "codex-mcp",
+    "codex-mcp-discovery",
+    "mcp-config",
+    "codex-vscode",
     "mcp-runtime",
     "codex-plugins",
     "codex-file-tree",

package/schemas/analysis-result.schema.json

@@ -81,6 +81,7 @@
         "codex_windows_helper_path",
         "codex_connectivity",
         "codex_remote_control",
+        "codex_mcp_discovery_mismatch",
         "codex_mcp_runtime",
         "codex_plugin_runtime",
         "codex_file_tree_ui",