ctxr-cli 0.19.0 → 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:
 
@@ -47,18 +44,16 @@ 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               15 contexture-owned skills (refreshed by `ctxr update`)
+  ctxr-*/SKILL.md               16 contexture-owned skills (refreshed by `ctxr update`)
   frontend-design/, eli5/       vendored third-party skills, with licenses and provenance
 .contexture/guidance/
   house-conventions.md        your store's own rules — inlined into AGENTS.md verbatim
@@ -97,7 +92,7 @@ Two distinctions make the rest of this readable:
 
 **`AGENTS.md`**, with six managed sections: *Store fundamentals* (root resolution, the frontmatter schema, the write path), *Mission*, *Retrieval: which leg to use*, *Capturing and ingesting*, *Placing a new note* (rendered from your actual taxonomy layers), and *Store conventions*.
 
-**The skills**, installed as full copies at `.agents/skills/ctxr-<name>/SKILL.md`. That path is the cross-harness canonical location; a harness that reads its own branded directory instead gets that directory bridged to it (`.claude/skills/` is a symlink), so skill auto-discovery works with no wrapper and no second copy. A harness without auto-discovery reaches the same file by path from `AGENTS.md`. They're contexture-owned — refreshed by `ctxr update`, never hand-edited — and they're written against *your* store's configured taxonomy, so no shipped profile's layer names leak into them. Your own skills live alongside, untouched by sync.
+**The skills**, installed as full copies at `.agents/skills/ctxr-<name>/SKILL.md`. That path is the cross-harness canonical location; a harness that reads its own branded directory instead gets that directory bridged to it (`.claude/skills/` is a symlink), so skill auto-discovery works with no wrapper and no second copy. A harness without auto-discovery reaches the same file by path from `AGENTS.md`. They're contexture-owned — refreshed by `ctxr update`, never hand-edited — and they're written against *your* store's configured taxonomy, so no shipped profile's layer names leak into them. Your own skills live alongside, untouched by sync. An owned skill may carry files beside its `SKILL.md` — `ctxr-second-opinion` ships the script that runs its reviewers — and update keeps that whole directory matching the package.
 
 | Skill | What it decides |
 | --- | --- |
@@ -115,6 +110,8 @@ Two distinctions make the rest of this readable:
 | `ctxr-submit` | Everything up to and including opening the pull request |
 | `ctxr-land` | Merging after review, and reclaiming the worktree |
 | `ctxr-session-capture` | What a finished session produced that is worth keeping |
+| `ctxr-upgrade` | Whether to upgrade the installed CLI now, and asking before it does |
+| `ctxr-second-opinion` | Whether a plan or a taste call needs three different model families, and how to weigh what they say |
 
 Your house rules go in `.contexture/guidance/house-conventions.md`. It's inlined into `AGENTS.md`'s *Store conventions* section in full, so it loads for every harness at the start of every session — there's no separate file an agent has to remember to open.
 
@@ -134,13 +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
 ```
 
 
@@ -186,7 +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
 
@@ -343,7 +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

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package/dist/commands/init.d.ts.map

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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/config/defaults.d.ts

@@ -28,17 +28,20 @@ export declare const DEFAULT_SKILLS_PATH = ".agents/skills/";
  */
 export declare const DEFAULT_VENDORED_SKILLS: readonly ['frontend-design', 'eli5'];
 /**
- * harness-portability spec: the guidance directory holding contexture's
- * shipped baseline convention file, the operator's own convention files
- * (inlined into AGENTS.md's "Store conventions" section — see
- * agents-doc.ts, from inline-conventions-and-mission), and (per
- * context-organize) the mission document.
+ * harness-portability spec: the guidance directory holding the operator's
+ * own convention files (inlined into AGENTS.md's "Store conventions" section
+ * after the shipped baseline, which is rendered there and never filed here —
+ * see agents-doc.ts) and (per context-organize) the mission document.
  */
 export declare const DEFAULT_GUIDANCE_PATH = ".contexture/guidance/";
-/** The shipped, contexture-owned baseline conventions — never hand-edited; refreshed by `ctxr update` like a skill copy. */
+/**
+ * Where earlier versions wrote the shipped baseline as a file in the guidance
+ * directory. It is now rendered straight into AGENTS.md; `removeManagedBaselineFile`
+ * deletes a copy left at this name when it still carries the managed-owner header.
+ */
 export declare const DEFAULT_BASELINE_CONVENTIONS_FILE_NAME = "baseline-conventions.md";
 /**
- * The baseline file's pre-rename name. `syncBaselineConventions` removes it
+ * The baseline file's pre-rename name. `removeManagedBaselineFile` removes it
  * when it still carries the managed-owner header, so the rename leaves no
  * orphan — the guidance directory is scanned wholesale, so an orphan would
  * be inlined into AGENTS.md a second time rather than merely sitting unused.

package/dist/config/defaults.d.ts.map

@@ -1 +1 @@
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package/dist/config/defaults.js

@@ -27,17 +27,20 @@ export const DEFAULT_SKILLS_PATH = '.agents/skills/';
  */
 export const DEFAULT_VENDORED_SKILLS = ['frontend-design', 'eli5'];
 /**
- * harness-portability spec: the guidance directory holding contexture's
- * shipped baseline convention file, the operator's own convention files
- * (inlined into AGENTS.md's "Store conventions" section — see
- * agents-doc.ts, from inline-conventions-and-mission), and (per
- * context-organize) the mission document.
+ * harness-portability spec: the guidance directory holding the operator's
+ * own convention files (inlined into AGENTS.md's "Store conventions" section
+ * after the shipped baseline, which is rendered there and never filed here —
+ * see agents-doc.ts) and (per context-organize) the mission document.
  */
 export const DEFAULT_GUIDANCE_PATH = '.contexture/guidance/';
-/** The shipped, contexture-owned baseline conventions — never hand-edited; refreshed by `ctxr update` like a skill copy. */
+/**
+ * Where earlier versions wrote the shipped baseline as a file in the guidance
+ * directory. It is now rendered straight into AGENTS.md; `removeManagedBaselineFile`
+ * deletes a copy left at this name when it still carries the managed-owner header.
+ */
 export const DEFAULT_BASELINE_CONVENTIONS_FILE_NAME = 'baseline-conventions.md';
 /**
- * The baseline file's pre-rename name. `syncBaselineConventions` removes it
+ * The baseline file's pre-rename name. `removeManagedBaselineFile` removes it
  * when it still carries the managed-owner header, so the rename leaves no
  * orphan — the guidance directory is scanned wholesale, so an orphan would
  * be inlined into AGENTS.md a second time rather than merely sitting unused.

package/dist/config/defaults.js.map

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package/dist/config/schema.js

@@ -263,9 +263,9 @@ const OrganizeSchema = z
 });
 /**
  * harness-portability spec: the portable skill pack and the guidance
- * documents (a shipped baseline convention file, the operator's own
- * convention files, and the mission document) AGENTS.md's generated
- * sections read from and inline.
+ * documents (the operator's own convention files and the mission document)
+ * AGENTS.md's generated sections read from and inline. The shipped baseline
+ * is rendered into AGENTS.md directly, never read from this directory.
  *
  * `skills_path` and `guidance_path` are the only spellings. Their pre-rename
  * names `procedures_path` and `conventions_path` were accepted here as inputs

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

@@ -1 +1 @@
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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) {