ctxr-cli 0.20.0 → 0.20.1

package/README.md

@@ -27,15 +27,12 @@ Running an agent harness in a container? [contexture-images](https://github.com/
 ```sh
 mkdir my-store && cd my-store
 ctxr init
-ctxr adapters generate   # writes the harness entry file (CLAUDE.md) and its permission config
 ```
 
 `ctxr init` asks two questions, then creates the git repository (if there isn't one), scaffolds the store, and commits it:
 
 - **Which taxonomy profile?** `para` (Projects / Areas / Resources / Archives — the default), `zettelkasten` (no layers at all; structure emerges from links), or `diataxis` (Tutorials / How-to / Reference / Explanation). Or bring your own layer list with `--taxonomy <file.yaml>`.
-- **Which agent harnesses?** `claude-code` (default — its adapter generates `CLAUDE.md` plus a `.claude/settings.json` wiring up the write-gate hook) and/or `hermes-agent` (reads `AGENTS.md` directly, so it needs no entry file at all). `--harness none` opts out.
-
-Harness adapter output is the one part `init` doesn't write itself, which is why `ctxr adapters generate` is a separate line above; `ctxr update` regenerates it from then on.
+- **Which agent harnesses?** `claude-code` (default — its adapter generates `CLAUDE.md`, a one-line import of `AGENTS.md`) and/or `hermes-agent` (reads `AGENTS.md` directly, so it needs no entry file at all). `--harness none` opts out.
 
 Non-interactively, pass them as flags — nothing ever blocks on a prompt:
 
@@ -47,15 +44,13 @@ ctxr init --profile para --harness claude-code
 
 ## What a store looks like on disk
 
-After `ctxr init --profile para`, plus `ctxr adapters generate`:
+After `ctxr init --profile para`:
 
 ```
 contexture.yaml               single source of truth — what this store chose; the rest takes shipped defaults
 AGENTS.md                     generated entry document — six managed sections
 CLAUDE.md                     harness entry file; a one-line managed import of AGENTS.md
 .claude/
-  settings.json               PreToolUse hook wiring for the write gate
-  hooks/                      the write-gate shim
   skills/ -> ../.agents/skills   a bridge, so Claude Code auto-discovers the canonical skills
 .agents/skills/               THE canonical skills location, read natively by most harnesses
   ctxr-*/SKILL.md               16 contexture-owned skills (refreshed by `ctxr update`)
@@ -136,13 +131,11 @@ flowchart LR
 
   S --> C --> K --> P --> U --> R --> L
 
-  G1["write-gate hook"]
   G2["pre-commit · pre-push"]
-  C -.- G1
   U -.- G2
 
   classDef gate fill:#fbfbfb,stroke:#bbb,stroke-dasharray:4 3,color:#666
-  class G1,G2 gate
+  class G2 gate
 ```
 
 
@@ -188,7 +181,7 @@ Each item is validated and applied independently, so one bad path refuses that i
 
 They're ordinary `git` and `gh`. The CLI owns only what git cannot do — creating the worktree, applying validated note writes, running the health gates — and the sequencing, the confirmation gates, and the judgment live in the skills, where you can read and change them. That's why `ctxr session` has exactly three subcommands: `start`, `capture`, and `list`.
 
-Three mechanical backstops hold the line underneath all of it: the **pre-commit** hook runs `doctor --staged`; the **pre-push** hook refuses a push to the default branch (`CONTEXTURE_ALLOW_DEFAULT_BRANCH_PUSH=1` is the emergency override, for emergencies); and for Claude Code the **write-gate** PreToolUse hook denies any edit under the store root made outside the active session worktree.
+Two mechanical backstops hold the line underneath all of it: the **pre-commit** hook runs `doctor --staged`, and the **pre-push** hook refuses a push to the default branch (`CONTEXTURE_ALLOW_DEFAULT_BRANCH_PUSH=1` is the emergency override, for emergencies). Both are version-controlled git hooks, so they hold whichever harness, or human, does the writing.
 
 ## The knowledge loop
 
@@ -345,7 +338,7 @@ To pin a value against a future default change, declare it. Nothing rewrites wha
 | `rollup gather \| write \| stale` | Entity synthesis: enumerate, write, find what's out of date |
 | `publish gather \| new \| check` | Resolve a subject, scaffold a page, run the structural gates |
 | `session start \| capture \| list` | Session worktrees, and applying an approved capture proposal |
-| `adapters generate \| write-gate` | Regenerate harness outputs; the write-gate hook target |
+| `adapters generate` | Regenerate harness outputs (`ctxr update` does this too) |
 | `serve` | Read the store in a browser |
 | `update` | Bring contexture-owned files up to the installed version |
 | `version [--check]` | Report the installed version; `--check` compares it against the latest published release |

package/dist/commands/adapters-generate.d.ts

@@ -1,23 +1,11 @@
 import type { CommandOutcome, CommandRequires } from '../core/command.js';
+import { type AdaptersGenerateFileResult } from '../core/adapter-outputs.js';
 import type { RunEnv } from '../core/env.js';
-import type { GitRunner } from '../core/git/exec.js';
 import type { Store } from '../core/store.js';
+export type { AdaptersGenerateFileResult } from '../core/adapter-outputs.js';
 export declare const requires: CommandRequires;
-export interface AdaptersGenerateFileResult {
-    path: string;
-    changed: boolean;
-}
 export interface AdaptersGenerateData {
     files: AdaptersGenerateFileResult[];
 }
-/**
- * adapters spec / task 8.3-8.4: every configured harness-generation adapter
- * gets its entry file's fenced region (re)written from `render()`, and,
- * for a harness that supports it, its permission config merged in. Two
- * adapters targeting the same physical file (the common case: one harness's
- * own entry file) never collide, because each owns a distinctly-named fence.
- */
-/** The generation itself, shared with `ctxr update`. */
-export declare function generateAdapterOutputs(git: GitRunner, store: Store): Promise<AdaptersGenerateFileResult[]>;
 export declare function execute(env: RunEnv, store: Store): Promise<CommandOutcome<AdaptersGenerateData>>;
 //# sourceMappingURL=adapters-generate.d.ts.map

package/dist/commands/adapters-generate.d.ts.map

@@ -1 +1 @@
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package/dist/commands/adapters-generate.js

@@ -1,56 +1,8 @@
-import path from 'node:path';
-import { configuredAdapters } from '../adapters/registry.js';
-import { agentsMdPath } from '../core/agents-doc.js';
+import { generateAdapterOutputs } from '../core/adapter-outputs.js';
 import { ExitCode } from '../core/exit-codes.js';
-import { upsertFencedRegionInFile } from '../core/fs/fenced-region.js';
-import { retireInstalledHookScript } from '../core/hooks.js';
-import { mergeJsonArrayLists } from '../core/json-config-merge.js';
-import { harnessEntryFence } from '../core/markers.js';
 export const requires = { store: 'required' };
-/**
- * adapters spec / task 8.3-8.4: every configured harness-generation adapter
- * gets its entry file's fenced region (re)written from `render()`, and,
- * for a harness that supports it, its permission config merged in. Two
- * adapters targeting the same physical file (the common case: one harness's
- * own entry file) never collide, because each owns a distinctly-named fence.
- */
-/** The generation itself, shared with `ctxr update`. */
-export async function generateAdapterOutputs(git, store) {
-    const files = [];
-    for (const adapter of configuredAdapters(store.config, 'harness-generation')) {
-        if (adapter.entryFileName !== undefined && adapter.render !== undefined) {
-            const entryPath = path.join(store.root, adapter.entryFileName);
-            const { changed } = await upsertFencedRegionInFile(entryPath, harnessEntryFence(adapter.id), adapter.render(agentsMdPath(store.root)));
-            files.push({ path: adapter.entryFileName, changed });
-        }
-        if (adapter.permissionConfig) {
-            const input = {
-                root: store.root,
-                worktreesPath: store.config.session.worktrees_path,
-            };
-            let permChanged = false;
-            // retire-the-write-gate: the script this adapter used to install is
-            // removed rather than left orphaned. contexture delivered it, so
-            // contexture takes it away; it is version-controlled, so an operator
-            // who wants it back has it in history.
-            for (const targetPath of adapter.permissionConfig.retiredHookFiles ?? []) {
-                const { changed: retired } = await retireInstalledHookScript(store.root, targetPath);
-                permChanged = permChanged || retired;
-            }
-            const permPath = path.join(store.root, adapter.permissionConfig.path);
-            const rules = adapter.permissionConfig.render(input);
-            const retired = adapter.permissionConfig.retiredRules(input);
-            const { changed: rulesChanged } = await mergeJsonArrayLists(permPath, rules, {
-                remove: retired,
-            });
-            permChanged = permChanged || rulesChanged;
-            files.push({ path: adapter.permissionConfig.path, changed: permChanged });
-        }
-    }
-    return files;
-}
 export async function execute(env, store) {
-    const files = await generateAdapterOutputs(env.git, store);
+    const files = await generateAdapterOutputs(store);
     const changedCount = files.filter((f) => f.changed).length;
     return {
         exitCode: ExitCode.Ok,

package/dist/commands/adapters-generate.js.map

@@ -1 +1 @@
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package/dist/commands/init.d.ts.map

@@ -1 +1 @@
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package/dist/commands/init.js

@@ -13,6 +13,7 @@ import { seedHouseConventionsFile } from '../core/convention-doc.js';
 import { syncNoteTemplates } from '../core/note-templates.js';
 import { syncShippedSkills, syncVendoredSkills } from '../core/skills.js';
 import { bridgeHarnessSkills } from '../core/harness/bridge.js';
+import { generateAdapterOutputs } from '../core/adapter-outputs.js';
 import { reconcileStore, WORKTREES_GITIGNORE_FENCE } from '../core/reconcile.js';
 import { isInteractive } from '../core/env.js';
 import { CLI_VERSION } from '../version.js';
@@ -246,6 +247,15 @@ async function runInitCore(env, flags) {
     const { changed: templateFilesCreated, findings: templateFindings } = await syncNoteTemplates(root, config, CLI_VERSION);
     findings.push(...templateFindings);
     await buildAgentsConventionsSection(root, config);
+    // init-generates-harness-adapter-output: the harnesses just selected get
+    // their entry files now, in the bootstrap commit, rather than waiting for a
+    // first `ctxr update`. After the last AGENTS.md writer, as in the reconcile.
+    // Only what the generator wrote is staged: an adapter that contributes
+    // nothing (claude-code's permission config) reports unchanged, so no empty
+    // file is created and `git add` is never handed a path that doesn't exist.
+    const adapterFilesCreated = (await generateAdapterOutputs({ root, config }))
+        .filter((f) => f.changed)
+        .map((f) => f.path);
     const guidanceFilesCreated = [
         ...(houseConventionsSeeded.created ? [path.join(config.harness.guidance_path, DEFAULT_HOUSE_CONVENTIONS_FILE_NAME)] : []),
         ...(missionSeeded ? [missionSeeded] : []),
@@ -288,6 +298,7 @@ async function runInitCore(env, flags) {
         ...templateFilesCreated,
         ...bridgedPaths,
         ...guidanceFilesCreated,
+        ...adapterFilesCreated,
         ...hookFiles,
     ]);
     const commitSha = await commitIfStaged(env.git, root, { kind: 'bootstrap' }, 'chore: initialize contexture store');
@@ -304,6 +315,7 @@ async function runInitCore(env, flags) {
                 ...vendoredSkillFilesCreated,
                 ...bridgedPaths,
                 ...guidanceFilesCreated,
+                ...adapterFilesCreated,
                 ...hookFiles,
             ],
             unchanged: [],

package/dist/commands/init.js.map

@@ -1 +1 @@
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package/dist/commands/update.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../src/commands/update.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AACvD,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAC1E,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAQ7C,OAAO,KAAK,EAAE,cAAc,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAK9D,eAAO,MAAM,QAAQ,EAAE,eAAuC,CAAC;AAE/D,MAAM,WAAW,UAAU;IACzB,uGAAuG;IACvG,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,uFAAuF;IACvF,QAAQ,CAAC,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,EAAE,EAAE,MAAM,CAAA;KAAE,CAAC;IACxC;;;OAGG;IACH,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,wEAAwE;IACxE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,oFAAoF;IACpF,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED;;;;;;GAMG;AACH,wBAAsB,OAAO,CAC3B,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,cAAc,EAAE,UAAU,GAAG,cAAc,CAAC,CAAC,GACxE,OAAO,CAAC,cAAc,CAAC,UAAU,CAAC,CAAC,CA0CrC;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,CAE5D;AAkBD;;;;;;;;;;;;;GAaG;AACH,wBAAsB,iBAAiB,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,cAAc,GAAG,OAAO,CAAC,cAAc,CAAC,UAAU,CAAC,CAAC,CAwD/G"}
+{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../src/commands/update.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AACvD,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAC1E,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAQ7C,OAAO,KAAK,EAAE,cAAc,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAI9D,eAAO,MAAM,QAAQ,EAAE,eAAuC,CAAC;AAE/D,MAAM,WAAW,UAAU;IACzB,uGAAuG;IACvG,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,uFAAuF;IACvF,QAAQ,CAAC,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,EAAE,EAAE,MAAM,CAAA;KAAE,CAAC;IACxC;;;OAGG;IACH,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,wEAAwE;IACxE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,oFAAoF;IACpF,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED;;;;;;GAMG;AACH,wBAAsB,OAAO,CAC3B,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,cAAc,EAAE,UAAU,GAAG,cAAc,CAAC,CAAC,GACxE,OAAO,CAAC,cAAc,CAAC,UAAU,CAAC,CAAC,CAwCrC;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,CAE5D;AAkBD;;;;;;;;;;;;;GAaG;AACH,wBAAsB,iBAAiB,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,cAAc,GAAG,OAAO,CAAC,cAAc,CAAC,UAAU,CAAC,CAAC,CAwD/G"}

package/dist/commands/update.js

@@ -9,7 +9,6 @@ import { CONFIG_FILE_NAME } from '../core/root.js';
 import { worktreePathFor } from '../core/session.js';
 import { updateAdvisory } from '../core/version-check.js';
 import { CLI_VERSION } from '../version.js';
-import { generateAdapterOutputs } from './adapters-generate.js';
 export const requires = { store: 'required' };
 /**
  * entry-doc-generation spec (D5): after upgrading contexture, bring every
@@ -30,12 +29,10 @@ export async function execute(env, store) {
         await writeFileAtomic(configPathFor(store.root), String(store.document));
     }
     const { changed, findings } = await reconcileStore(env, store.root, store.config);
-    const adapterFiles = await generateAdapterOutputs(env.git, store);
     const all = [
         ...new Set([
             ...(migrated ? [CONFIG_FILE_NAME] : []),
             ...changed,
-            ...adapterFiles.filter((f) => f.changed).map((f) => f.path),
         ]),
     ];
     // cli-contract: the human path for the release advisory. This is the command

package/dist/commands/update.js.map

@@ -1 +1 @@
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package/dist/core/adapter-outputs.d.ts

@@ -0,0 +1,19 @@
+import type { Store } from './store.js';
+export interface AdaptersGenerateFileResult {
+    path: string;
+    changed: boolean;
+}
+/**
+ * adapters spec / task 8.3-8.4: every configured harness-generation adapter
+ * gets its entry file's fenced region (re)written from `render()`, and,
+ * for a harness that supports it, its permission config merged in. Two
+ * adapters targeting the same physical file (the common case: one harness's
+ * own entry file) never collide, because each owns a distinctly-named fence.
+ */
+/**
+ * The generation itself, shared by `ctxr adapters generate`, `reconcileStore`
+ * (so `ctxr update` and `ctxr init` on an existing store), and a fresh
+ * `ctxr init` (init-generates-harness-adapter-output).
+ */
+export declare function generateAdapterOutputs(store: Store): Promise<AdaptersGenerateFileResult[]>;
+//# sourceMappingURL=adapter-outputs.d.ts.map

package/dist/core/adapter-outputs.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"adapter-outputs.d.ts","sourceRoot":"","sources":["../../src/core/adapter-outputs.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AAExC,MAAM,WAAW,0BAA0B;IACzC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,OAAO,CAAC;CAClB;AAED;;;;;;GAMG;AACH;;;;GAIG;AACH,wBAAsB,sBAAsB,CAAC,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,0BAA0B,EAAE,CAAC,CA2ChG"}

package/dist/core/adapter-outputs.js

@@ -0,0 +1,54 @@
+import path from 'node:path';
+import { configuredAdapters } from '../adapters/registry.js';
+import { agentsMdPath } from './agents-doc.js';
+import { upsertFencedRegionInFile } from './fs/fenced-region.js';
+import { retireInstalledHookScript } from './hooks.js';
+import { mergeJsonArrayLists } from './json-config-merge.js';
+import { harnessEntryFence } from './markers.js';
+/**
+ * adapters spec / task 8.3-8.4: every configured harness-generation adapter
+ * gets its entry file's fenced region (re)written from `render()`, and,
+ * for a harness that supports it, its permission config merged in. Two
+ * adapters targeting the same physical file (the common case: one harness's
+ * own entry file) never collide, because each owns a distinctly-named fence.
+ */
+/**
+ * The generation itself, shared by `ctxr adapters generate`, `reconcileStore`
+ * (so `ctxr update` and `ctxr init` on an existing store), and a fresh
+ * `ctxr init` (init-generates-harness-adapter-output).
+ */
+export async function generateAdapterOutputs(store) {
+    const files = [];
+    for (const adapter of configuredAdapters(store.config, 'harness-generation')) {
+        if (adapter.entryFileName !== undefined && adapter.render !== undefined) {
+            const entryPath = path.join(store.root, adapter.entryFileName);
+            const { changed } = await upsertFencedRegionInFile(entryPath, harnessEntryFence(adapter.id), adapter.render(agentsMdPath(store.root)));
+            files.push({ path: adapter.entryFileName, changed });
+        }
+        if (adapter.permissionConfig) {
+            const input = {
+                root: store.root,
+                worktreesPath: store.config.session.worktrees_path,
+            };
+            let permChanged = false;
+            // retire-the-write-gate: the script this adapter used to install is
+            // removed rather than left orphaned. contexture delivered it, so
+            // contexture takes it away; it is version-controlled, so an operator
+            // who wants it back has it in history.
+            for (const targetPath of adapter.permissionConfig.retiredHookFiles ?? []) {
+                const { changed: retired } = await retireInstalledHookScript(store.root, targetPath);
+                permChanged = permChanged || retired;
+            }
+            const permPath = path.join(store.root, adapter.permissionConfig.path);
+            const rules = adapter.permissionConfig.render(input);
+            const retired = adapter.permissionConfig.retiredRules(input);
+            const { changed: rulesChanged } = await mergeJsonArrayLists(permPath, rules, {
+                remove: retired,
+            });
+            permChanged = permChanged || rulesChanged;
+            files.push({ path: adapter.permissionConfig.path, changed: permChanged });
+        }
+    }
+    return files;
+}
+//# sourceMappingURL=adapter-outputs.js.map

package/dist/core/adapter-outputs.js.map

@@ -0,0 +1 @@
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package/dist/core/agents-doc.d.ts.map

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package/dist/core/agents-doc.js

@@ -62,7 +62,9 @@ function collapseNestedPrefixes(prefixes) {
 }
 export function renderLegRoutingSection(config) {
     const exclusions = collapseNestedPrefixes(excludedPrefixesFor(config));
-    return substituteBlock(agentsTemplate('retrieval-leg-routing').replaceAll('__GRAPH_DOCUMENT_PATH__', GRAPH_DOCUMENT_RELATIVE_PATH), '__EXCLUSION_PATHS__', [exclusions.map((prefix) => `\`${prefix}\``).join(', ')]).split('\n');
+    return substituteBlock(agentsTemplate('retrieval-leg-routing')
+        .replaceAll('__GRAPH_DOCUMENT_PATH__', GRAPH_DOCUMENT_RELATIVE_PATH)
+        .replaceAll('__CAPTURE_ROOT__', config.ingest.capture_root), '__EXCLUSION_PATHS__', [exclusions.map((prefix) => `\`${prefix}\``).join(', ')]).split('\n');
 }
 /** Idempotently reconciles AGENTS.md's leg-routing section from current config — called at init and on re-init. */
 export async function buildAgentsLegRoutingSection(root, config) {

package/dist/core/agents-doc.js.map

@@ -1 +1 @@
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package/dist/core/reconcile.d.ts

@@ -11,7 +11,8 @@ export interface ReconcileResult {
 /**
  * Brings every contexture-OWNED file in a store to the installed package's
  * version: the managed .gitignore blocks, every generated AGENTS.md
- * section, the contexture-owned skill copies, and the git hooks. Operator
+ * section, the contexture-owned skill copies, every declared harness's
+ * adapter outputs, and the git hooks. Operator
  * content is never rewritten. Shared by `ctxr init` (reconciling an
  * existing store) and `ctxr update` (after upgrading contexture).
  * Byte-stable: a second run with nothing changed writes nothing.

package/dist/core/reconcile.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"reconcile.d.ts","sourceRoot":"","sources":["../../src/core/reconcile.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAEvD,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,UAAU,CAAC;AAWvC,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,eAAe,CAAC;AAS7C,eAAO,MAAM,yBAAyB,8BAA4B,CAAC;AAwBnE,MAAM,WAAW,eAAe;IAC9B,+EAA+E;IAC/E,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,2EAA2E;IAC3E,QAAQ,EAAE,OAAO,EAAE,CAAC;CACrB;AAED;;;;;;;GAOG;AACH,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,eAAe,CAAC,CAsE7G"}
+{"version":3,"file":"reconcile.d.ts","sourceRoot":"","sources":["../../src/core/reconcile.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAGvD,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,UAAU,CAAC;AAWvC,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,eAAe,CAAC;AAS7C,eAAO,MAAM,yBAAyB,8BAA4B,CAAC;AAwBnE,MAAM,WAAW,eAAe;IAC9B,+EAA+E;IAC/E,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,2EAA2E;IAC3E,QAAQ,EAAE,OAAO,EAAE,CAAC;CACrB;AAED;;;;;;;;GAQG;AACH,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,eAAe,CAAC,CA2E7G"}

package/dist/core/reconcile.js

@@ -1,6 +1,7 @@
 import path from 'node:path';
 import { DEFAULT_BASELINE_CONVENTIONS_FILE_NAME } from '../config/defaults.js';
 import { CLI_VERSION } from '../version.js';
+import { generateAdapterOutputs } from './adapter-outputs.js';
 import { agentsMdPath, AGENTS_MD_SECTION_ORDER, buildAgentsCanonicalSection, buildAgentsCaptureSection, buildAgentsConventionsSection, buildAgentsLegRoutingSection, buildAgentsMissionSection, buildAgentsPlacementSection, } from './agents-doc.js';
 import { removeManagedBaselineFile } from './convention-doc.js';
 import { removeFencedRegionFromFile, reorderFencedRegionsInFile, upsertFencedRegionInFile } from './fs/fenced-region.js';
@@ -33,7 +34,8 @@ const RETIRED_AGENTS_MD_STORE_CONVENTIONS_FENCE = htmlCommentFence('store-conven
 /**
  * Brings every contexture-OWNED file in a store to the installed package's
  * version: the managed .gitignore blocks, every generated AGENTS.md
- * section, the contexture-owned skill copies, and the git hooks. Operator
+ * section, the contexture-owned skill copies, every declared harness's
+ * adapter outputs, and the git hooks. Operator
  * content is never rewritten. Shared by `ctxr init` (reconciling an
  * existing store) and `ctxr update` (after upgrading contexture).
  * Byte-stable: a second run with nothing changed writes nothing.
@@ -95,6 +97,11 @@ export async function reconcileStore(env, root, config) {
     if ((await reorderFencedRegionsInFile(agentsMdPath(root), AGENTS_MD_SECTION_ORDER)).changed)
         agentsChanged = true;
     note('AGENTS.md', agentsChanged);
+    // init-generates-harness-adapter-output: inside the shared reconcile, not
+    // beside it, so `ctxr init` on an existing store cannot miss it again the
+    // way it did when only `ctxr update` called the generator.
+    for (const file of await generateAdapterOutputs({ root, config }))
+        note(file.path, file.changed);
     const { changed: hookFiles } = await installHooks(root, config.git.default_branch);
     changed.push(...hookFiles);
     await configureHooksPath(env.git, root);

package/dist/core/reconcile.js.map

@@ -1 +1 @@
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package/dist/core/skills.d.ts.map

@@ -1 +1 @@
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package/dist/core/skills.js

@@ -125,7 +125,10 @@ const CAPTURE = {
     file: 'ctxr-capture',
     name: 'Capture',
     description: 'Bring material from outside the store into the inbox as a faithful record carrying its source identity, then hand off to ingest.',
-    body: (config) => skillTemplate('ctxr-capture').replaceAll('__INBOX_PATH__', config.ingest.inbox_path).split('\n'),
+    body: (config) => skillTemplate('ctxr-capture')
+        .replaceAll('__INBOX_PATH__', config.ingest.inbox_path)
+        .replaceAll('__CAPTURE_ROOT__', config.ingest.capture_root)
+        .split('\n'),
 };
 const INGEST_ORCHESTRATION = {
     file: 'ctxr-ingest-orchestration',

package/dist/core/skills.js.map

@@ -1 +1 @@
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package/dist/version.d.ts

@@ -1,5 +1,5 @@
 /** Kept in sync with package.json's "version" field. */
-export declare const CLI_VERSION = "0.20.0";
+export declare const CLI_VERSION = "0.20.1";
 /**
  * The npm package this executable is published as. Bound here, beside the
  * version, because the release check resolves the latest published release by

package/dist/version.js

@@ -1,5 +1,5 @@
 /** Kept in sync with package.json's "version" field. */
-export const CLI_VERSION = '0.20.0';
+export const CLI_VERSION = '0.20.1';
 /**
  * The npm package this executable is published as. Bound here, beside the
  * version, because the release check resolves the latest published release by

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ctxr-cli",
-  "version": "0.20.0",
+  "version": "0.20.1",
   "description": "Context store for AI coding agents — markdown and git, catalog and graph retrieval, no vector database.",
   "type": "module",
   "license": "MIT",

package/templates/agents/canonical.md

@@ -14,6 +14,8 @@ The worktree step is why a command run inside a session worktree operates on tha
 
 A new note starts from a template under `__TEMPLATES_PATH__`, not from a blank file and not by copying whatever sibling happens to be nearby. Substitute `{{title}}` and `{{date}}` as you write it — no command expands them, and a note that lands with one still in it is reported by `ctxr lint`. A template is never a note: nothing under that path is catalogued, graphed, or retrieved. Add your own kinds there alongside the shipped ones; contexture only ever rewrites the ones it delivered.
 
+Every shipped template except the base, `Note`, stamps the kind it is for into the note's `tags`. Keep it when you start a note: it is how you find every note of a kind, with your own search, since no `ctxr` command filters by it. A kind you cut from the base should stamp its own name the same way, and any further tags are this store's own.
+
 ### Write path
 
 Every write to this store happens inside a session worktree, never directly on the default branch: `ctxr session start` creates one, and the work stays there for as long as the session runs. When the operator asks to wrap up, `ctxr-submit` validates with `ctxr doctor`, commits, pushes, and opens (or reports how to open) a pull request — that request is what triggers it, not having finished a piece of work. Do not edit files in the store root directly.

package/templates/agents/retrieval-leg-routing.md

@@ -36,5 +36,11 @@ __EXCLUSION_PATHS__
 
 Feed anything it finds back in as `--seed` to pick the pass up again from there.
 
+Those exclusions are for finding knowledge. Captures under `__CAPTURE_ROOT__` are left out because they
+are provenance, not notes, so a search scoped this way never finds one. When the question is whether
+the store already holds some material — a document, a meeting, a thread — search `__CAPTURE_ROOT__`
+directly, by content and by the `capture_file` a capture names. Finding nothing in the notes is not
+evidence that it was never captured.
+
 There is no `ctxr search` command. Nothing here takes a free-text query, and no result carries a
 relevance score. Ranked or semantic search is deferred to a future version — do not look for one.

package/templates/notes/Concept.md

@@ -1,7 +1,8 @@
 ---
 date_created: "{{date}}"
 title: "{{title}}"
-tags: []
+tags:
+  - Concept
 ---
 # {{title}}
 

package/templates/skills/ctxr-capture.md

@@ -47,7 +47,9 @@ markdown, not at the bytes.
 ## 4. Check before you write it into the inbox
 
 If the material may already be in the store, run `ctxr source check <path> --source-id <id>` and read
-the verdict before going further. Re-capturing something the store already holds is how one source ends
+the verdict before going further. That check compares material you already hold; before fetching
+anything, search `__CAPTURE_ROOT__` for it by content and by `capture_file`. The retrieval pass leaves
+that directory out, so a search scoped by it will never find a capture. Re-capturing something the store already holds is how one source ends
 up cited twice under two identities.
 
 Then write the file into `__INBOX_PATH__`. Nothing else — no note, no edit to an existing note, no

package/templates/skills/ctxr-publish.md

@@ -99,9 +99,17 @@ before reporting the page as ready. It answers only what's derivable from the fi
 in step 1, the form and reader choices in step 5, and factual accuracy stay judgment calls, not checker output.
 
 `ctxr publish new` and `ctxr publish check` each end by naming the address `ctxr serve` answers for
-this page. Open it and look at the page before you hand it on. Whether the form works, whether the
-prose reads, whether it renders at all is exactly what the checks above cannot answer, and it is
-cheapest to fix while the page is still yours.
+this page. Look at the page before you hand it on. Whether the form works, whether the prose reads,
+whether it renders at all is exactly what the checks above cannot answer, and it is cheapest to fix
+while the page is still yours.
+
+That address may be served from another host, or behind an access proxy, where you cannot reach it.
+You do not need it: from this machine, start `ctxr serve` in the background, open the address it
+prints followed by the page's route in your browser tool, and stop the server when you are done. A
+page still in a session worktree is served there under its previewable route, the same as anywhere
+else. If you have no way to see a rendered page, say in your hand-off that it has not been checked
+visually, so whoever reviews it knows they are the first to look. Never report a page as ready on the
+strength of `ctxr publish check` alone.
 
 A page written in a session worktree is previewable rather than published, because the
 published-pages address reads the store's own checkout and the page has not reached it yet. That
@@ -110,6 +118,11 @@ previewable address stops answering the moment the worktree is reclaimed — the
 Report the address you actually opened, and say which of the two it is, so nobody is handed a link
 that is about to change.
 
+Both addresses are full URLs when the store declares `serve.base_url` in `contexture.yaml`, and bare
+routes such as `/preview/…` when it does not. A bare route is not a link anyone else can open. Do not
+guess a host to put in front of it: hand on the route as it is, and tell the operator that declaring
+`serve.base_url` would make every address a command reports a link.
+
 ## 7. It's a page, not a note
 
 The published-pages location is excluded from retrieval by default — a page never becomes a source for

package/templates/skills/ctxr-second-opinion/lenses.md

@@ -12,4 +12,6 @@ drop one: a collapsed pair adds cost and no breadth.
 - **brand-strategist** — long-term positioning, category ownership, how it ages.
 
 A store may add its own lens inline as `Name:description`, for example
-`"Plainspoken:blunt, substance first, distrusts slogans"`.
+`"Plainspoken:blunt, substance first, distrusts slogans"`. The description may contain commas. A comma starts
+the next lens only when the text after it is exactly a lens name above or begins `Name:`, so keep colons out
+of a description.

package/templates/skills/ctxr-second-opinion/run.mjs

@@ -33,19 +33,30 @@ const MAX_ARGV_BYTES = 120_000;
 
 const env = (name, fallback) => process.env[`CTXR_SECOND_OPINION_${name}`] || fallback;
 
-/** Model choice lives here, in one table. Override by environment, never by editing a store. */
+/**
+ * Model choice lives here, in one table. Override by environment, never by editing a store.
+ *
+ * Effort is each provider's own recommended default, not one this runner picked:
+ *  - claude: no --effort at all, so Claude Code applies its own default for the model.
+ *  - codex: `medium`, the default its model catalog declares (`default_reasoning_level`). It is passed
+ *    explicitly because the flag cannot simply be left off: with no pin in config.toml, codex resolves to
+ *    `reasoning effort: none` on a ChatGPT login (seen 2026-10-05), which is no review at all. `low` at the
+ *    `fast` tier. A machine that pins its own effort in config.toml is overridden by this; set
+ *    CTXR_SECOND_OPINION_CODEX_EFFORT to use another.
+ *  - agy: the effort is part of the model name; `(High)` is Gemini's default thinking level.
+ * For scale: on one short plan Claude took 35 s at `high` and 514 s at `max`, so a deeper pass is a choice
+ * (CTXR_SECOND_OPINION_CLAUDE_EFFORT=max), not something to leave on by default.
+ */
 function tiers() {
   return {
     strong: {
-      // `high`, not `max`: the same two-and-a-half-thousand-character plan took Claude 35 s at `high` and 514 s at
-      // `max` (and once timed out at 280 s), with a valid critique both times. `max` stays one variable away.
-      claude: { model: env('CLAUDE_MODEL', 'opus'), effort: env('CLAUDE_EFFORT', 'high') },
-      codex: { effort: env('CODEX_EFFORT', 'xhigh') },
+      claude: { model: env('CLAUDE_MODEL', 'opus'), effort: env('CLAUDE_EFFORT', null) },
+      codex: { effort: env('CODEX_EFFORT', 'medium') },
       agy: { model: env('AGY_MODEL', 'Gemini 3.1 Pro (High)') },
     },
     fast: {
-      claude: { model: env('CLAUDE_MODEL', 'haiku'), effort: null },
-      codex: { effort: env('CODEX_EFFORT', 'medium') },
+      claude: { model: env('CLAUDE_MODEL', 'haiku'), effort: env('CLAUDE_EFFORT', null) },
+      codex: { effort: env('CODEX_EFFORT', 'low') },
       agy: { model: env('AGY_MODEL', 'Gemini 3.8 Flash (High)') },
     },
   };
@@ -54,10 +65,11 @@ function tiers() {
 /**
  * The flags this runner passes, so preflight can confirm each CLI's --help still lists them. Only flags
  * the help text documents belong here: `claude` still accepts a hidden --max-turns, but with `--tools ""`
- * there is no tool turn to bound, so it is not passed at all.
+ * there is no tool turn to bound, so it is not passed at all. --effort is not listed because it is only
+ * passed when the environment asks for one.
  */
 const FLAGS_USED = {
-  claude: { helpArgs: ['--help'], flags: ['--tools', '--model', '--effort', '--no-session-persistence', '--disable-slash-commands', '--output-format'] },
+  claude: { helpArgs: ['--help'], flags: ['--tools', '--model', '--no-session-persistence', '--disable-slash-commands', '--output-format'] },
   codex: { helpArgs: ['exec', '--help'], flags: ['--skip-git-repo-check', '--sandbox', '--ephemeral', '--color', '--config'] },
   agy: { helpArgs: ['--help'], flags: ['--print', '--sandbox', '--disable-slash-commands', '--model'] },
 };
@@ -267,13 +279,28 @@ function loadLensRoster() {
   return roster;
 }
 
+/**
+ * Splits `--lens` into one string per lens. Lenses are comma-separated, but an inline description may itself
+ * contain commas: a fragment starts a NEW lens only when it is exactly a roster name or begins `Name:`;
+ * any other fragment continues the lens before it. So `minimalist,House taste:blunt, anti-slogan` is two
+ * lenses, and a description must not contain a colon (that would read as the start of another lens).
+ */
+export function splitLenses(spec, roster) {
+  const lenses = [];
+  for (const fragment of spec.split(',').map((f) => f.trim()).filter(Boolean)) {
+    const startsLens = roster.has(fragment.toLowerCase()) || /^[^:,]{1,40}:/.test(fragment);
+    if (startsLens || lenses.length === 0) lenses.push(fragment);
+    else lenses[lenses.length - 1] += `, ${fragment}`;
+  }
+  return lenses;
+}
+
 function lensBlock(spec) {
   const roster = loadLensRoster();
-  const specs = spec.split(',').map((s) => s.trim()).filter(Boolean);
   const described = [];
-  for (const s of specs) {
+  for (const s of splitLenses(spec, roster)) {
     if (roster.has(s.toLowerCase())) described.push(`- ${s.toLowerCase()} — ${roster.get(s.toLowerCase())}`);
-    else if (s.includes(':')) {
+    else if (/^[^:,]{1,40}:/.test(s)) {
       const [name, ...rest] = s.split(':');
       described.push(`- ${name.trim()} — ${rest.join(':').trim()}`);
     } else throw new UsageError(`unknown lens "${s}" (known: ${[...roster.keys()].join(', ')}; or pass "Name:description")`);

package/templates/skills/ctxr-second-opinion.md

@@ -82,11 +82,17 @@ nothing in the plan, so it was written without reading it; it does not count. **
 two valid critiques: say so at the top of your answer and do not call anything a consensus.
 
 Add `--tier fast` to drop each family to a cheaper model, for a plan that is small and easy to redo. The
-default tier is right for anything the operator will act on. A default critique usually takes under a minute
-and costs a few tens of cents. Claude's highest effort setting (`CTXR_SECOND_OPINION_CLAUDE_EFFORT=max`) is
-a deliberate deep pass, not a default: on the same short plan it took over eight minutes where the default
-took half a minute, and it is the one setting that can reach the runner's ten-minute limit. Start such a run
-in the background and tell the operator it is under way.
+default tier is right for anything the operator will act on.
+
+Each reviewer runs at its provider's own recommended default effort, not one this skill chose. Claude gets no
+effort setting, so Claude Code applies its default for the model. Codex gets `medium`, the default its model
+catalog declares; the runner passes it explicitly because Codex left to itself, with no setting pinned, can
+resolve to no reasoning at all. Gemini's effort is part of its model name, and `High` is its default. Measured on a
+short plan, a default critique took about 40 seconds in all, 30 to 37 seconds per reviewer, and costs a few tens
+of cents. A deeper pass is a choice: set `CTXR_SECOND_OPINION_CLAUDE_EFFORT=max` and Claude alone took over
+eight minutes on the same plan, close enough to the runner's ten-minute limit that you should start such a run
+in the background and tell the operator it is under way. A machine that pins its own Codex effort in its
+configuration is overridden by `medium`; set `CTXR_SECOND_OPINION_CODEX_EFFORT` to use another.
 
 ## 4. Synthesize on the letters first
 
@@ -150,7 +156,9 @@ This mode names its files by model, because what you are reading is whether the
 To get breadth as well as model diversity, add `--lens` with two or three taste lenses. Each model then
 answers as every lens in one response, giving a lens-by-model grid. The built-in lenses are minimalist,
 marketer, contrarian, end-user and brand-strategist. A store's own lens goes in as `Name:description`, for
-example `--lens "minimalist,Plainspoken:blunt and substance first"`. Choose lenses that pull in different
+example `--lens "minimalist,Plainspoken:blunt, substance first, distrusts slogans"`. A description may contain
+commas: a comma starts the next lens only when what follows is a built-in lens name or begins `Name:`. So a
+description must not contain a colon. Choose lenses that pull in different
 directions; if two would obviously agree, drop one.
 
 Read a lens grid on both axes. Down a column (one lens across the three models) agreement means that