@codyswann/lisa 2.325.0 → 2.325.2

package/dist/core/upstream-evidence-manifest.js

@@ -424,8 +424,8 @@ export const UPSTREAM_EVIDENCE_MANIFEST = Object.freeze({
     "plugins/src/base/skills/lisa-debrief-apply/SKILL.md": "90c5f01994bb0f8e71947e8a2f765ccf9a6aa3da47b8d7b8e2022150ef89c2b2",
     "plugins/src/base/skills/lisa-debrief/SKILL.md": "47e4cda36b07994ff47ab15fb04a17dd6b0c310ad804f9cae9d69637edaaa72a",
     "plugins/src/base/skills/lisa-delivery-effectiveness/SKILL.md": "21bc55fa0e86a9694bd22269fd089dbfae0c54c199262f46a4955447acea0f35",
-    "plugins/src/base/skills/lisa-detect-tooling/SKILL.md": "e29b3b8ebc256468bb67e5d10e2ae3cb4eda9ba20dfd2e065201b00864134734",
-    "plugins/src/base/skills/lisa-detect-tooling/scripts/detect-tooling.mjs": "043c3f59d6a7a21a3ab4fce8ae8dc88e8650c19c5a57bba40f567c5257684747",
+    "plugins/src/base/skills/lisa-detect-tooling/SKILL.md": "1778a009d06099b3bd2d9a33b37bec34836b295e21fad220ae926491d3557208",
+    "plugins/src/base/skills/lisa-detect-tooling/scripts/detect-tooling.mjs": "ccbd2cf7251e792467ca74c664088a22b1c50ead579ad2279a55daa5d0ba0693",
     "plugins/src/base/skills/lisa-doctor/SKILL.md": "fb41a1e63c5332d47a46e715aff52551f3df867033b5e4f37dfaeee30019b891",
     "plugins/src/base/skills/lisa-drive-pr-to-merge/SKILL.md": "c78ae2ba32c830d0b2cd7d24de91adf99e2b3cef4c7cab1c417580d86f41351f",
     "plugins/src/base/skills/lisa-epic-triage/SKILL.md": "d02760411249bddbd396f283191fe3e82bb7b95bf9393a19a7025dc5a57c3ab7",

package/package.json

@@ -115,7 +115,7 @@
     "brace-expansion": ">=5.0.9"
   },
   "name": "@codyswann/lisa",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "Claude Code governance framework that applies guardrails, guidance, and automated enforcement to projects",
   "main": "dist/index.js",
   "exports": {

package/plugins/lisa/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "Universal governance — agents, skills, commands, hooks, and rules for all projects",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "Universal governance: agents, skills, commands, hooks, and rules for all projects.",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa/.codex-plugin/skills/lisa-detect-tooling/SKILL.md

@@ -13,7 +13,7 @@ Lisa provisions tooling through four unrelated mechanisms, and only one of them
 | playwright, stryker | npm devDependency from a stack template | nothing — a local `node_modules` binary |
 | maestro | npm **scripts** in the Expo template | **nothing** |
 | sonar | `src/sonar/sonar-installer.ts` | nothing |
-| linear | MCP server | nothing, and it needs browser OAuth |
+| linear | MCP server or `LINEAR_API_KEY` | `lisa-linear-access`, not a CLI |
 | bws, gh | `remoteEnv.tools` — pinned and checksummed | this, and only this |
 
 Nothing populates that last row. So a project can ship scripts that invoke `maestro`, wire an MCP server whose CLI it also shells out to, and configure Playwright thresholds, while the manifest that actually provisions binaries stays empty — and every one of those fails at the moment of use rather than at setup.
@@ -25,7 +25,7 @@ That is the same failure this repository has now paid for twice: `gh` was declar
 Reads four signals, subtracts what `remoteEnv.tools` already declares, and prints what is left with the evidence for each:
 
 - **npm scripts** that invoke a binary. The strongest signal there is — a script running `maestro test` is the project stating a dependency in executable form. Matched on the script *body*, not its name, because the name is a label.
-- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one.
+- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one. Do not infer a CLI for access layers that already define their own headless substrate; Linear is handled by `lisa-linear-access` through `LINEAR_API_KEY` + GraphQL when MCP OAuth is unavailable.
 - **Credential usage notes.** A note explaining what a token is for usually names the program that consumes it. `lisa-secrets-access` already exposes these without touching a value, which makes them a first-class input rather than a trick.
 - **Quality configuration**, where a threshold implies the tool that produces it.
 

package/plugins/lisa/.codex-plugin/skills/lisa-detect-tooling/scripts/detect-tooling.mjs

@@ -51,8 +51,13 @@ const KNOWN_TOOLS = Object.freeze({
     viaNpm: "@playwright/test",
   },
   linear: {
-    why: "Linear is wired as an MCP server, which needs browser OAuth and so cannot authenticate in a container.",
+    why: "Linear reaches a container through lisa-linear-access with LINEAR_API_KEY; only the MCP path needs browser OAuth, and there is no official CLI to pin.",
     mcpFallback: "linear-server",
+    // No official Linear CLI exists, so no proposal can name one. Kept even
+    // though the substrate allowlist normally removes Linear before this
+    // point: a second signal reaching here must not resurrect a binary that
+    // does not exist.
+    noCli: true,
   },
 });
 
@@ -99,12 +104,43 @@ export function toolsFromScripts(pkg) {
 }
 
 /**
- * Tools implied by MCP servers that also have a CLI.
+ * MCP servers that are access substrates rather than evidence for a CLI.
  *
- * An MCP server is not a substitute for the binary. Several authenticate by
- * browser OAuth, which a container cannot do at all, so a project relying on one
- * remotely has no integration rather than a degraded one — the CLI is the form
- * that survives the trip.
+ * Linear is the important case: Lisa's `lisa-linear-access` skill owns the
+ * headless path through `LINEAR_API_KEY` + GraphQL. There is no official Linear
+ * CLI to pin, and the unrelated `linear` npm package is not a tracker binary.
+ * Treating the MCP server as CLI evidence would push operators toward an
+ * arbitrary third-party executable instead of the access-layer contract.
+ */
+/** Prefix marking evidence that shows a path is missing, not what fills it. */
+const MCP_EVIDENCE = "MCP";
+
+/** What to ask when the only evidence is an MCP-only integration. */
+const REMOTE_PATH_QUESTION =
+  "no manifest entry proposed — confirm how this reaches a container: a CLI, " +
+  "a key-authenticated API call, or deliberately local-only";
+
+const MCP_ACCESS_LAYER_SUBSTRATES = Object.freeze({
+  "linear-server":
+    "lisa-linear-access uses LINEAR_API_KEY in headless sessions",
+});
+
+/**
+ * Integrations wired only as an MCP server — the weakest signal here, and the
+ * easiest to over-read.
+ *
+ * True: an MCP server that authenticates interactively cannot authenticate in a
+ * container, so THAT path does not survive the trip.
+ *
+ * Not implied: that the integration is unavailable, or that a CLI is the
+ * answer. Linear proves both halves — its MCP server needs browser OAuth, and
+ * its GraphQL API is key-authenticated, so `lisa-linear-access` already reaches
+ * it headlessly with LINEAR_API_KEY and there is no official CLI to pin at all.
+ * A server whose access layer owns headless auth is skipped entirely.
+ *
+ * For anything else, this raises a QUESTION rather than asserting a need: this
+ * integration has no remote path as configured, confirm it has one. The answer
+ * may be a CLI, may be a direct API call, and may be "local-only on purpose".
  * @param {object|null} mcp Parsed .mcp.json.
  * @returns {Map<string, string>} Tool name to the server that implies it.
  */
@@ -114,10 +150,19 @@ export function toolsFromMcp(mcp) {
   for (const [tool, meta] of Object.entries(KNOWN_TOOLS)) {
     if (!meta.mcpFallback) continue;
     const server = servers.find(name => name.includes(meta.mcpFallback));
+    if (
+      server &&
+      Object.keys(MCP_ACCESS_LAYER_SUBSTRATES).some(substrate =>
+        server.includes(substrate)
+      )
+    ) {
+      continue;
+    }
     if (server) {
       found.set(
         tool,
-        `MCP server "${server}" (browser OAuth cannot run remotely)`
+        `${MCP_EVIDENCE} server "${server}" — an interactively authenticated ` +
+          `MCP server has no remote path; confirm this integration has one`
       );
     }
   }
@@ -241,6 +286,17 @@ export function detectTooling(cwd = process.cwd()) {
  * @returns {{install: object[], require: object[]}} Manifest skeletons.
  */
 export function proposedEntries(proposal) {
+  // Whether a binary can be proposed is a fact about the TOOL, not about how it
+  // was detected. Keying this on "the evidence was an MCP server" suppressed
+  // exactly the wrong case: the substrate allowlist already removes Linear
+  // before it becomes evidence, so the only tools reaching that branch were
+  // ones like Maestro that genuinely do have a CLI — the binary the Expo
+  // template invokes and nothing installs.
+  //
+  // So the question is asked only where there is no pinnable CLI to name.
+  if (KNOWN_TOOLS[proposal.name]?.noCli) {
+    return { install: [], require: [], question: REMOTE_PATH_QUESTION };
+  }
   const viaNpm = KNOWN_TOOLS[proposal.name]?.viaNpm;
   if (viaNpm) {
     // npm resolves per platform, so one entry serves every surface.
@@ -295,6 +351,7 @@ if (process.argv[1] && import.meta.url === `file://${process.argv[1]}`) {
         console.log(`    evidence: ${evidence}`);
       }
       const entries = proposedEntries(proposal);
+      if (entries.question) console.log(`    ${entries.question}`);
       for (const entry of entries.install) {
         console.log(`    tools.install: ${JSON.stringify(entry)}`);
       }

package/plugins/lisa/skills/lisa-detect-tooling/SKILL.md

@@ -13,7 +13,7 @@ Lisa provisions tooling through four unrelated mechanisms, and only one of them
 | playwright, stryker | npm devDependency from a stack template | nothing — a local `node_modules` binary |
 | maestro | npm **scripts** in the Expo template | **nothing** |
 | sonar | `src/sonar/sonar-installer.ts` | nothing |
-| linear | MCP server | nothing, and it needs browser OAuth |
+| linear | MCP server or `LINEAR_API_KEY` | `lisa-linear-access`, not a CLI |
 | bws, gh | `remoteEnv.tools` — pinned and checksummed | this, and only this |
 
 Nothing populates that last row. So a project can ship scripts that invoke `maestro`, wire an MCP server whose CLI it also shells out to, and configure Playwright thresholds, while the manifest that actually provisions binaries stays empty — and every one of those fails at the moment of use rather than at setup.
@@ -25,7 +25,7 @@ That is the same failure this repository has now paid for twice: `gh` was declar
 Reads four signals, subtracts what `remoteEnv.tools` already declares, and prints what is left with the evidence for each:
 
 - **npm scripts** that invoke a binary. The strongest signal there is — a script running `maestro test` is the project stating a dependency in executable form. Matched on the script *body*, not its name, because the name is a label.
-- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one.
+- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one. Do not infer a CLI for access layers that already define their own headless substrate; Linear is handled by `lisa-linear-access` through `LINEAR_API_KEY` + GraphQL when MCP OAuth is unavailable.
 - **Credential usage notes.** A note explaining what a token is for usually names the program that consumes it. `lisa-secrets-access` already exposes these without touching a value, which makes them a first-class input rather than a trick.
 - **Quality configuration**, where a threshold implies the tool that produces it.
 

package/plugins/lisa/skills/lisa-detect-tooling/scripts/detect-tooling.mjs

@@ -51,8 +51,13 @@ const KNOWN_TOOLS = Object.freeze({
     viaNpm: "@playwright/test",
   },
   linear: {
-    why: "Linear is wired as an MCP server, which needs browser OAuth and so cannot authenticate in a container.",
+    why: "Linear reaches a container through lisa-linear-access with LINEAR_API_KEY; only the MCP path needs browser OAuth, and there is no official CLI to pin.",
     mcpFallback: "linear-server",
+    // No official Linear CLI exists, so no proposal can name one. Kept even
+    // though the substrate allowlist normally removes Linear before this
+    // point: a second signal reaching here must not resurrect a binary that
+    // does not exist.
+    noCli: true,
   },
 });
 
@@ -99,12 +104,43 @@ export function toolsFromScripts(pkg) {
 }
 
 /**
- * Tools implied by MCP servers that also have a CLI.
+ * MCP servers that are access substrates rather than evidence for a CLI.
  *
- * An MCP server is not a substitute for the binary. Several authenticate by
- * browser OAuth, which a container cannot do at all, so a project relying on one
- * remotely has no integration rather than a degraded one — the CLI is the form
- * that survives the trip.
+ * Linear is the important case: Lisa's `lisa-linear-access` skill owns the
+ * headless path through `LINEAR_API_KEY` + GraphQL. There is no official Linear
+ * CLI to pin, and the unrelated `linear` npm package is not a tracker binary.
+ * Treating the MCP server as CLI evidence would push operators toward an
+ * arbitrary third-party executable instead of the access-layer contract.
+ */
+/** Prefix marking evidence that shows a path is missing, not what fills it. */
+const MCP_EVIDENCE = "MCP";
+
+/** What to ask when the only evidence is an MCP-only integration. */
+const REMOTE_PATH_QUESTION =
+  "no manifest entry proposed — confirm how this reaches a container: a CLI, " +
+  "a key-authenticated API call, or deliberately local-only";
+
+const MCP_ACCESS_LAYER_SUBSTRATES = Object.freeze({
+  "linear-server":
+    "lisa-linear-access uses LINEAR_API_KEY in headless sessions",
+});
+
+/**
+ * Integrations wired only as an MCP server — the weakest signal here, and the
+ * easiest to over-read.
+ *
+ * True: an MCP server that authenticates interactively cannot authenticate in a
+ * container, so THAT path does not survive the trip.
+ *
+ * Not implied: that the integration is unavailable, or that a CLI is the
+ * answer. Linear proves both halves — its MCP server needs browser OAuth, and
+ * its GraphQL API is key-authenticated, so `lisa-linear-access` already reaches
+ * it headlessly with LINEAR_API_KEY and there is no official CLI to pin at all.
+ * A server whose access layer owns headless auth is skipped entirely.
+ *
+ * For anything else, this raises a QUESTION rather than asserting a need: this
+ * integration has no remote path as configured, confirm it has one. The answer
+ * may be a CLI, may be a direct API call, and may be "local-only on purpose".
  * @param {object|null} mcp Parsed .mcp.json.
  * @returns {Map<string, string>} Tool name to the server that implies it.
  */
@@ -114,10 +150,19 @@ export function toolsFromMcp(mcp) {
   for (const [tool, meta] of Object.entries(KNOWN_TOOLS)) {
     if (!meta.mcpFallback) continue;
     const server = servers.find(name => name.includes(meta.mcpFallback));
+    if (
+      server &&
+      Object.keys(MCP_ACCESS_LAYER_SUBSTRATES).some(substrate =>
+        server.includes(substrate)
+      )
+    ) {
+      continue;
+    }
     if (server) {
       found.set(
         tool,
-        `MCP server "${server}" (browser OAuth cannot run remotely)`
+        `${MCP_EVIDENCE} server "${server}" — an interactively authenticated ` +
+          `MCP server has no remote path; confirm this integration has one`
       );
     }
   }
@@ -241,6 +286,17 @@ export function detectTooling(cwd = process.cwd()) {
  * @returns {{install: object[], require: object[]}} Manifest skeletons.
  */
 export function proposedEntries(proposal) {
+  // Whether a binary can be proposed is a fact about the TOOL, not about how it
+  // was detected. Keying this on "the evidence was an MCP server" suppressed
+  // exactly the wrong case: the substrate allowlist already removes Linear
+  // before it becomes evidence, so the only tools reaching that branch were
+  // ones like Maestro that genuinely do have a CLI — the binary the Expo
+  // template invokes and nothing installs.
+  //
+  // So the question is asked only where there is no pinnable CLI to name.
+  if (KNOWN_TOOLS[proposal.name]?.noCli) {
+    return { install: [], require: [], question: REMOTE_PATH_QUESTION };
+  }
   const viaNpm = KNOWN_TOOLS[proposal.name]?.viaNpm;
   if (viaNpm) {
     // npm resolves per platform, so one entry serves every surface.
@@ -295,6 +351,7 @@ if (process.argv[1] && import.meta.url === `file://${process.argv[1]}`) {
         console.log(`    evidence: ${evidence}`);
       }
       const entries = proposedEntries(proposal);
+      if (entries.question) console.log(`    ${entries.question}`);
       for (const entry of entries.install) {
         console.log(`    tools.install: ${JSON.stringify(entry)}`);
       }

package/plugins/lisa-agy/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "Universal governance — agents, skills, commands, hooks, and rules for all projects",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa-agy/skills/lisa-detect-tooling/SKILL.md

@@ -13,7 +13,7 @@ Lisa provisions tooling through four unrelated mechanisms, and only one of them
 | playwright, stryker | npm devDependency from a stack template | nothing — a local `node_modules` binary |
 | maestro | npm **scripts** in the Expo template | **nothing** |
 | sonar | `src/sonar/sonar-installer.ts` | nothing |
-| linear | MCP server | nothing, and it needs browser OAuth |
+| linear | MCP server or `LINEAR_API_KEY` | `lisa-linear-access`, not a CLI |
 | bws, gh | `remoteEnv.tools` — pinned and checksummed | this, and only this |
 
 Nothing populates that last row. So a project can ship scripts that invoke `maestro`, wire an MCP server whose CLI it also shells out to, and configure Playwright thresholds, while the manifest that actually provisions binaries stays empty — and every one of those fails at the moment of use rather than at setup.
@@ -25,7 +25,7 @@ That is the same failure this repository has now paid for twice: `gh` was declar
 Reads four signals, subtracts what `remoteEnv.tools` already declares, and prints what is left with the evidence for each:
 
 - **npm scripts** that invoke a binary. The strongest signal there is — a script running `maestro test` is the project stating a dependency in executable form. Matched on the script *body*, not its name, because the name is a label.
-- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one.
+- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one. Do not infer a CLI for access layers that already define their own headless substrate; Linear is handled by `lisa-linear-access` through `LINEAR_API_KEY` + GraphQL when MCP OAuth is unavailable.
 - **Credential usage notes.** A note explaining what a token is for usually names the program that consumes it. `lisa-secrets-access` already exposes these without touching a value, which makes them a first-class input rather than a trick.
 - **Quality configuration**, where a threshold implies the tool that produces it.
 

package/plugins/lisa-agy/skills/lisa-detect-tooling/scripts/detect-tooling.mjs

@@ -51,8 +51,13 @@ const KNOWN_TOOLS = Object.freeze({
     viaNpm: "@playwright/test",
   },
   linear: {
-    why: "Linear is wired as an MCP server, which needs browser OAuth and so cannot authenticate in a container.",
+    why: "Linear reaches a container through lisa-linear-access with LINEAR_API_KEY; only the MCP path needs browser OAuth, and there is no official CLI to pin.",
     mcpFallback: "linear-server",
+    // No official Linear CLI exists, so no proposal can name one. Kept even
+    // though the substrate allowlist normally removes Linear before this
+    // point: a second signal reaching here must not resurrect a binary that
+    // does not exist.
+    noCli: true,
   },
 });
 
@@ -99,12 +104,43 @@ export function toolsFromScripts(pkg) {
 }
 
 /**
- * Tools implied by MCP servers that also have a CLI.
+ * MCP servers that are access substrates rather than evidence for a CLI.
  *
- * An MCP server is not a substitute for the binary. Several authenticate by
- * browser OAuth, which a container cannot do at all, so a project relying on one
- * remotely has no integration rather than a degraded one — the CLI is the form
- * that survives the trip.
+ * Linear is the important case: Lisa's `lisa-linear-access` skill owns the
+ * headless path through `LINEAR_API_KEY` + GraphQL. There is no official Linear
+ * CLI to pin, and the unrelated `linear` npm package is not a tracker binary.
+ * Treating the MCP server as CLI evidence would push operators toward an
+ * arbitrary third-party executable instead of the access-layer contract.
+ */
+/** Prefix marking evidence that shows a path is missing, not what fills it. */
+const MCP_EVIDENCE = "MCP";
+
+/** What to ask when the only evidence is an MCP-only integration. */
+const REMOTE_PATH_QUESTION =
+  "no manifest entry proposed — confirm how this reaches a container: a CLI, " +
+  "a key-authenticated API call, or deliberately local-only";
+
+const MCP_ACCESS_LAYER_SUBSTRATES = Object.freeze({
+  "linear-server":
+    "lisa-linear-access uses LINEAR_API_KEY in headless sessions",
+});
+
+/**
+ * Integrations wired only as an MCP server — the weakest signal here, and the
+ * easiest to over-read.
+ *
+ * True: an MCP server that authenticates interactively cannot authenticate in a
+ * container, so THAT path does not survive the trip.
+ *
+ * Not implied: that the integration is unavailable, or that a CLI is the
+ * answer. Linear proves both halves — its MCP server needs browser OAuth, and
+ * its GraphQL API is key-authenticated, so `lisa-linear-access` already reaches
+ * it headlessly with LINEAR_API_KEY and there is no official CLI to pin at all.
+ * A server whose access layer owns headless auth is skipped entirely.
+ *
+ * For anything else, this raises a QUESTION rather than asserting a need: this
+ * integration has no remote path as configured, confirm it has one. The answer
+ * may be a CLI, may be a direct API call, and may be "local-only on purpose".
  * @param {object|null} mcp Parsed .mcp.json.
  * @returns {Map<string, string>} Tool name to the server that implies it.
  */
@@ -114,10 +150,19 @@ export function toolsFromMcp(mcp) {
   for (const [tool, meta] of Object.entries(KNOWN_TOOLS)) {
     if (!meta.mcpFallback) continue;
     const server = servers.find(name => name.includes(meta.mcpFallback));
+    if (
+      server &&
+      Object.keys(MCP_ACCESS_LAYER_SUBSTRATES).some(substrate =>
+        server.includes(substrate)
+      )
+    ) {
+      continue;
+    }
     if (server) {
       found.set(
         tool,
-        `MCP server "${server}" (browser OAuth cannot run remotely)`
+        `${MCP_EVIDENCE} server "${server}" — an interactively authenticated ` +
+          `MCP server has no remote path; confirm this integration has one`
       );
     }
   }
@@ -241,6 +286,17 @@ export function detectTooling(cwd = process.cwd()) {
  * @returns {{install: object[], require: object[]}} Manifest skeletons.
  */
 export function proposedEntries(proposal) {
+  // Whether a binary can be proposed is a fact about the TOOL, not about how it
+  // was detected. Keying this on "the evidence was an MCP server" suppressed
+  // exactly the wrong case: the substrate allowlist already removes Linear
+  // before it becomes evidence, so the only tools reaching that branch were
+  // ones like Maestro that genuinely do have a CLI — the binary the Expo
+  // template invokes and nothing installs.
+  //
+  // So the question is asked only where there is no pinnable CLI to name.
+  if (KNOWN_TOOLS[proposal.name]?.noCli) {
+    return { install: [], require: [], question: REMOTE_PATH_QUESTION };
+  }
   const viaNpm = KNOWN_TOOLS[proposal.name]?.viaNpm;
   if (viaNpm) {
     // npm resolves per platform, so one entry serves every surface.
@@ -295,6 +351,7 @@ if (process.argv[1] && import.meta.url === `file://${process.argv[1]}`) {
         console.log(`    evidence: ${evidence}`);
       }
       const entries = proposedEntries(proposal);
+      if (entries.question) console.log(`    ${entries.question}`);
       for (const entry of entries.install) {
         console.log(`    tools.install: ${JSON.stringify(entry)}`);
       }

package/plugins/lisa-cdk/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa-cdk",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "AWS CDK-specific plugin",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa-cdk/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa-cdk",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "AWS CDK-specific Lisa plugin.",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa-cdk-agy/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa-cdk",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "AWS CDK-specific plugin",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa-cdk-copilot/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa-cdk",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "AWS CDK-specific plugin",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa-cdk-cursor/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa-cdk",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "AWS CDK-specific plugin",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa-copilot/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "Universal governance — agents, skills, commands, hooks, and rules for all projects",
   "author": {
     "name": "Cody Swann"

package/plugins/lisa-copilot/skills/lisa-detect-tooling/SKILL.md

@@ -13,7 +13,7 @@ Lisa provisions tooling through four unrelated mechanisms, and only one of them
 | playwright, stryker | npm devDependency from a stack template | nothing — a local `node_modules` binary |
 | maestro | npm **scripts** in the Expo template | **nothing** |
 | sonar | `src/sonar/sonar-installer.ts` | nothing |
-| linear | MCP server | nothing, and it needs browser OAuth |
+| linear | MCP server or `LINEAR_API_KEY` | `lisa-linear-access`, not a CLI |
 | bws, gh | `remoteEnv.tools` — pinned and checksummed | this, and only this |
 
 Nothing populates that last row. So a project can ship scripts that invoke `maestro`, wire an MCP server whose CLI it also shells out to, and configure Playwright thresholds, while the manifest that actually provisions binaries stays empty — and every one of those fails at the moment of use rather than at setup.
@@ -25,7 +25,7 @@ That is the same failure this repository has now paid for twice: `gh` was declar
 Reads four signals, subtracts what `remoteEnv.tools` already declares, and prints what is left with the evidence for each:
 
 - **npm scripts** that invoke a binary. The strongest signal there is — a script running `maestro test` is the project stating a dependency in executable form. Matched on the script *body*, not its name, because the name is a label.
-- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one.
+- **MCP servers with a CLI equivalent.** An MCP server is not a substitute for the binary: several authenticate by browser OAuth, which a container cannot do, so a project relying on one remotely has *no* integration rather than a degraded one. Do not infer a CLI for access layers that already define their own headless substrate; Linear is handled by `lisa-linear-access` through `LINEAR_API_KEY` + GraphQL when MCP OAuth is unavailable.
 - **Credential usage notes.** A note explaining what a token is for usually names the program that consumes it. `lisa-secrets-access` already exposes these without touching a value, which makes them a first-class input rather than a trick.
 - **Quality configuration**, where a threshold implies the tool that produces it.
 

package/plugins/lisa-copilot/skills/lisa-detect-tooling/scripts/detect-tooling.mjs

@@ -51,8 +51,13 @@ const KNOWN_TOOLS = Object.freeze({
     viaNpm: "@playwright/test",
   },
   linear: {
-    why: "Linear is wired as an MCP server, which needs browser OAuth and so cannot authenticate in a container.",
+    why: "Linear reaches a container through lisa-linear-access with LINEAR_API_KEY; only the MCP path needs browser OAuth, and there is no official CLI to pin.",
     mcpFallback: "linear-server",
+    // No official Linear CLI exists, so no proposal can name one. Kept even
+    // though the substrate allowlist normally removes Linear before this
+    // point: a second signal reaching here must not resurrect a binary that
+    // does not exist.
+    noCli: true,
   },
 });
 
@@ -99,12 +104,43 @@ export function toolsFromScripts(pkg) {
 }
 
 /**
- * Tools implied by MCP servers that also have a CLI.
+ * MCP servers that are access substrates rather than evidence for a CLI.
  *
- * An MCP server is not a substitute for the binary. Several authenticate by
- * browser OAuth, which a container cannot do at all, so a project relying on one
- * remotely has no integration rather than a degraded one — the CLI is the form
- * that survives the trip.
+ * Linear is the important case: Lisa's `lisa-linear-access` skill owns the
+ * headless path through `LINEAR_API_KEY` + GraphQL. There is no official Linear
+ * CLI to pin, and the unrelated `linear` npm package is not a tracker binary.
+ * Treating the MCP server as CLI evidence would push operators toward an
+ * arbitrary third-party executable instead of the access-layer contract.
+ */
+/** Prefix marking evidence that shows a path is missing, not what fills it. */
+const MCP_EVIDENCE = "MCP";
+
+/** What to ask when the only evidence is an MCP-only integration. */
+const REMOTE_PATH_QUESTION =
+  "no manifest entry proposed — confirm how this reaches a container: a CLI, " +
+  "a key-authenticated API call, or deliberately local-only";
+
+const MCP_ACCESS_LAYER_SUBSTRATES = Object.freeze({
+  "linear-server":
+    "lisa-linear-access uses LINEAR_API_KEY in headless sessions",
+});
+
+/**
+ * Integrations wired only as an MCP server — the weakest signal here, and the
+ * easiest to over-read.
+ *
+ * True: an MCP server that authenticates interactively cannot authenticate in a
+ * container, so THAT path does not survive the trip.
+ *
+ * Not implied: that the integration is unavailable, or that a CLI is the
+ * answer. Linear proves both halves — its MCP server needs browser OAuth, and
+ * its GraphQL API is key-authenticated, so `lisa-linear-access` already reaches
+ * it headlessly with LINEAR_API_KEY and there is no official CLI to pin at all.
+ * A server whose access layer owns headless auth is skipped entirely.
+ *
+ * For anything else, this raises a QUESTION rather than asserting a need: this
+ * integration has no remote path as configured, confirm it has one. The answer
+ * may be a CLI, may be a direct API call, and may be "local-only on purpose".
  * @param {object|null} mcp Parsed .mcp.json.
  * @returns {Map<string, string>} Tool name to the server that implies it.
  */
@@ -114,10 +150,19 @@ export function toolsFromMcp(mcp) {
   for (const [tool, meta] of Object.entries(KNOWN_TOOLS)) {
     if (!meta.mcpFallback) continue;
     const server = servers.find(name => name.includes(meta.mcpFallback));
+    if (
+      server &&
+      Object.keys(MCP_ACCESS_LAYER_SUBSTRATES).some(substrate =>
+        server.includes(substrate)
+      )
+    ) {
+      continue;
+    }
     if (server) {
       found.set(
         tool,
-        `MCP server "${server}" (browser OAuth cannot run remotely)`
+        `${MCP_EVIDENCE} server "${server}" — an interactively authenticated ` +
+          `MCP server has no remote path; confirm this integration has one`
       );
     }
   }
@@ -241,6 +286,17 @@ export function detectTooling(cwd = process.cwd()) {
  * @returns {{install: object[], require: object[]}} Manifest skeletons.
  */
 export function proposedEntries(proposal) {
+  // Whether a binary can be proposed is a fact about the TOOL, not about how it
+  // was detected. Keying this on "the evidence was an MCP server" suppressed
+  // exactly the wrong case: the substrate allowlist already removes Linear
+  // before it becomes evidence, so the only tools reaching that branch were
+  // ones like Maestro that genuinely do have a CLI — the binary the Expo
+  // template invokes and nothing installs.
+  //
+  // So the question is asked only where there is no pinnable CLI to name.
+  if (KNOWN_TOOLS[proposal.name]?.noCli) {
+    return { install: [], require: [], question: REMOTE_PATH_QUESTION };
+  }
   const viaNpm = KNOWN_TOOLS[proposal.name]?.viaNpm;
   if (viaNpm) {
     // npm resolves per platform, so one entry serves every surface.
@@ -295,6 +351,7 @@ if (process.argv[1] && import.meta.url === `file://${process.argv[1]}`) {
         console.log(`    evidence: ${evidence}`);
       }
       const entries = proposedEntries(proposal);
+      if (entries.question) console.log(`    ${entries.question}`);
       for (const entry of entries.install) {
         console.log(`    tools.install: ${JSON.stringify(entry)}`);
       }

package/plugins/lisa-cursor/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "lisa",
-  "version": "2.325.0",
+  "version": "2.325.2",
   "description": "Universal governance — agents, skills, commands, hooks, and rules for all projects",
   "author": {
     "name": "Cody Swann"