ctxr-cli 0.3.0 → 0.4.1

package/dist/adapters/harness/claude-code.d.ts

@@ -1,9 +1,3 @@
 import type { HarnessGenerationAdapter } from '../types.js';
-/**
- * The reference harness-generation adapter. Claude Code loads `@path`
- * references in its memory files, so the generated entry file's whole job
- * is one `@AGENTS.md` line — no convention text is duplicated here, only
- * imported (harness-portability spec's "entry file only imports" rule).
- */
 export declare const claudeCodeHarnessAdapter: HarnessGenerationAdapter;
 //# sourceMappingURL=claude-code.d.ts.map

package/dist/adapters/harness/claude-code.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"claude-code.d.ts","sourceRoot":"","sources":["../../../src/adapters/harness/claude-code.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,aAAa,CAAC;AAE5D;;;;;GAKG;AACH,eAAO,MAAM,wBAAwB,EAAE,wBAoDtC,CAAC"}
+{"version":3,"file":"claude-code.d.ts","sourceRoot":"","sources":["../../../src/adapters/harness/claude-code.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,wBAAwB,EAAyB,MAAM,aAAa,CAAC;AAYnF,eAAO,MAAM,wBAAwB,EAAE,wBAwEtC,CAAC"}

package/dist/adapters/harness/claude-code.js

@@ -5,6 +5,8 @@ import path from 'node:path';
  * is one `@AGENTS.md` line — no convention text is duplicated here, only
  * imported (harness-portability spec's "entry file only imports" rule).
  */
+/** Store-relative — where the generated write-gate hook script lands. */
+const HOOK_TARGET_PATH = '.claude/hooks/claude-code-write-gate.sh';
 export const claudeCodeHarnessAdapter = {
     id: 'claude-code',
     kind: 'harness-generation',
@@ -15,41 +17,58 @@ export const claudeCodeHarnessAdapter = {
     },
     permissionConfig: {
         path: '.claude/settings.json',
+        hookFile: {
+            templateFileName: 'claude-code-write-gate.sh',
+            targetPath: HOOK_TARGET_PATH,
+        },
         /**
-         * task 8.4: deny Write/Edit outside the active session worktree, and
-         * deny raw `git push`/`git commit` — the whole point of the worktree +
-         * PR write-lifecycle is that neither happens directly. The worktree
-         * PATH varies per session, but its PARENT prefix (worktreesPath) does
-         * not, so an allow-rule scoped to that whole prefix covers "the active
-         * session worktree" generically without needing to know which one is
-         * currently checked out.
+         * task 8.4 (revised): deny raw `git push`/`git commit`, and deny an
+         * edit anywhere under the store root except the active session
+         * worktree via a PreToolUse hook rather than a permission rule.
          *
-         * Rules are anchored at the store's absolute root (Claude Code's `//`
-         * absolute-path syntax), not written cwd-relative (`./`): a `./`-relative
-         * rule resolves against whatever directory a session's cwd happens to be
-         * at launch, which for a harness that opens a worktree itself as the
-         * project root (cwd already inside the worktree, not at the store root)
-         * resolves to the wrong directory — `./**` then denies the whole
-         * worktree and the `./<worktreesPath>/**` carve-out never matches
-         * anything, since there is no nested worktrees directory inside a
-         * worktree. An absolute anchor matches the real target path regardless
-         * of launch cwd, correctly covering both conventions.
+         * A permission rule cannot express that carve-out: Claude Code
+         * evaluates deny before allow with no exception mechanism ("a deny rule
+         * can't carry allowlist exceptions"), and the default session worktree
+         * path is nested INSIDE the store root, so a tree-wide deny would also
+         * cover the worktree an allow rule was meant to carve back out — which
+         * is exactly the bug this replaces (see proposal.md). A hook resolves
+         * the real target path at call time instead, so it has no such gap.
          *
-         * This targets Claude Code's settings.json permission-rule syntax as
-         * documented at the time this was written; if that syntax changes, this
-         * is the one function to update.
+         * `ctxr adapters write-gate` (the hook's target) does the actual
+         * decision, reusing `sanctionedPath`'s path resolution via
+         * `isWriteInScope` (write-lifecycle/path-gate.ts) so this and the
+         * pre-commit path allowlist can never disagree about what counts as an
+         * escape.
+         */
+        render({ root }) {
+            return {
+                permissions: {
+                    deny: ['Bash(git push:*)', 'Bash(git commit:*)'],
+                },
+                hooks: {
+                    PreToolUse: [
+                        {
+                            matcher: 'Edit|Write|NotebookEdit',
+                            hooks: [{ type: 'command', command: path.join(root, HOOK_TARGET_PATH) }],
+                        },
+                    ],
+                },
+            };
+        },
+        /**
+         * The deny/allow pair a previous release emitted for the same
+         * `{root, worktreesPath}` — reconstructed here (not read back off disk)
+         * so `mergeJsonArrayLists` can remove it by exact match, repairing a
+         * store whose config was generated before this fix.
          */
-        render({ root, worktreesPath }) {
-            // Claude Code's `//` absolute-path marker stands in for the path's own
-            // leading slash — strip it here so the result is `//abs/path`, not
-            // `///abs/path`.
+        retiredRules({ root, worktreesPath }) {
             const absRoot = root.replace(/^\/+/, '').replace(/\/+$/, '');
             const worktreesSegment = worktreesPath.replace(/^\/+|\/+$/g, '');
             const rootGlob = `//${absRoot}/**`;
             const worktreeGlob = `//${absRoot}/${worktreesSegment}/**`;
             return {
                 permissions: {
-                    deny: [`Write(${rootGlob})`, `Edit(${rootGlob})`, 'Bash(git push:*)', 'Bash(git commit:*)'],
+                    deny: [`Write(${rootGlob})`, `Edit(${rootGlob})`],
                     allow: [`Write(${worktreeGlob})`, `Edit(${worktreeGlob})`],
                 },
             };

package/dist/adapters/harness/claude-code.js.map

@@ -1 +1 @@
-{"version":3,"file":"claude-code.js","sourceRoot":"","sources":["../../../src/adapters/harness/claude-code.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAG7B;;;;;GAKG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAA6B;IAChE,EAAE,EAAE,aAAa;IACjB,IAAI,EAAE,oBAAoB;IAC1B,gBAAgB,EAAE,CAAC;IACnB,aAAa,EAAE,WAAW;IAE1B,MAAM,CAAC,YAAoB;QACzB,OAAO,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,EAAE,CAAC,CAAC;IAC7C,CAAC;IAED,gBAAgB,EAAE;QAChB,IAAI,EAAE,uBAAuB;QAC7B;;;;;;;;;;;;;;;;;;;;;;;WAuBG;QACH,MAAM,CAAC,EAAE,IAAI,EAAE,aAAa,EAA2C;YACrE,uEAAuE;YACvE,mEAAmE;YACnE,iBAAiB;YACjB,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;YAC7D,MAAM,gBAAgB,GAAG,aAAa,CAAC,OAAO,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;YACjE,MAAM,QAAQ,GAAG,KAAK,OAAO,KAAK,CAAC;YACnC,MAAM,YAAY,GAAG,KAAK,OAAO,IAAI,gBAAgB,KAAK,CAAC;YAC3D,OAAO;gBACL,WAAW,EAAE;oBACX,IAAI,EAAE,CAAC,SAAS,QAAQ,GAAG,EAAE,QAAQ,QAAQ,GAAG,EAAE,kBAAkB,EAAE,oBAAoB,CAAC;oBAC3F,KAAK,EAAE,CAAC,SAAS,YAAY,GAAG,EAAE,QAAQ,YAAY,GAAG,CAAC;iBAC3D;aACF,CAAC;QACJ,CAAC;KACF;CACF,CAAC"}
+{"version":3,"file":"claude-code.js","sourceRoot":"","sources":["../../../src/adapters/harness/claude-code.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAG7B;;;;;GAKG;AAEH,yEAAyE;AACzE,MAAM,gBAAgB,GAAG,yCAAyC,CAAC;AAEnE,MAAM,CAAC,MAAM,wBAAwB,GAA6B;IAChE,EAAE,EAAE,aAAa;IACjB,IAAI,EAAE,oBAAoB;IAC1B,gBAAgB,EAAE,CAAC;IACnB,aAAa,EAAE,WAAW;IAE1B,MAAM,CAAC,YAAoB;QACzB,OAAO,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,EAAE,CAAC,CAAC;IAC7C,CAAC;IAED,gBAAgB,EAAE;QAChB,IAAI,EAAE,uBAAuB;QAE7B,QAAQ,EAAE;YACR,gBAAgB,EAAE,2BAA2B;YAC7C,UAAU,EAAE,gBAAgB;SAC7B;QAED;;;;;;;;;;;;;;;;;;WAkBG;QACH,MAAM,CAAC,EAAE,IAAI,EAAyB;YACpC,OAAO;gBACL,WAAW,EAAE;oBACX,IAAI,EAAE,CAAC,kBAAkB,EAAE,oBAAoB,CAAC;iBACjD;gBACD,KAAK,EAAE;oBACL,UAAU,EAAE;wBACV;4BACE,OAAO,EAAE,yBAAyB;4BAClC,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,OAAO,EAAE,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,gBAAgB,CAAC,EAAE,CAAC;yBACzE;qBACF;iBACF;aACF,CAAC;QACJ,CAAC;QAED;;;;;WAKG;QACH,YAAY,CAAC,EAAE,IAAI,EAAE,aAAa,EAAyB;YACzD,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;YAC7D,MAAM,gBAAgB,GAAG,aAAa,CAAC,OAAO,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;YACjE,MAAM,QAAQ,GAAG,KAAK,OAAO,KAAK,CAAC;YACnC,MAAM,YAAY,GAAG,KAAK,OAAO,IAAI,gBAAgB,KAAK,CAAC;YAC3D,OAAO;gBACL,WAAW,EAAE;oBACX,IAAI,EAAE,CAAC,SAAS,QAAQ,GAAG,EAAE,QAAQ,QAAQ,GAAG,CAAC;oBACjD,KAAK,EAAE,CAAC,SAAS,YAAY,GAAG,EAAE,QAAQ,YAAY,GAAG,CAAC;iBAC3D;aACF,CAAC;QACJ,CAAC;KACF;CACF,CAAC"}

package/dist/adapters/types.d.ts

@@ -28,6 +28,20 @@ export declare const SUPPORTED_ADAPTER_INTERFACE_VERSION: Record<AdapterKind, nu
  * placed inside contexture's managed fenced region in that file — never the
  * whole file, so a hand-authored preamble outside the fence survives.
  */
+/**
+ * `root` is the store's absolute filesystem path. Permission-rule paths are
+ * anchored there (not written cwd-relative) because a session may be
+ * launched with its cwd already inside a worktree rather than at the store
+ * root — a cwd-relative rule would then resolve against the wrong directory.
+ * `binPath` is this installation's own resolved CLI entrypoint, for a
+ * harness whose config needs to shell out back to `ctxr` (a generated hook
+ * script). See claude-code.ts's permissionConfig for the concrete case.
+ */
+export interface PermissionConfigInput {
+    root: string;
+    worktreesPath: string;
+    binPath: string;
+}
 export interface HarnessGenerationAdapter extends Adapter<'harness-generation'> {
     /** The harness-specific file this adapter writes, relative to the store root (e.g. "CLAUDE.md"). */
     entryFileName: string;
@@ -36,17 +50,22 @@ export interface HarnessGenerationAdapter extends Adapter<'harness-generation'>
     permissionConfig?: {
         /** Relative to the store root (e.g. ".claude/settings.json"). */
         path: string;
+        render(input: PermissionConfigInput): Record<string, unknown>;
         /**
-         * `root` is the store's absolute filesystem path. Permission-rule paths
-         * are anchored there (not written cwd-relative) because a session may be
-         * launched with its cwd already inside a worktree rather than at the
-         * store root — a cwd-relative rule would then resolve against the wrong
-         * directory. See claude-code.ts's permissionConfig for the concrete case.
+         * Rules a previous release of this adapter emitted that the current
+         * `render()` no longer does — removed by exact match before the current
+         * rules are merged in, so a store whose config was generated by an
+         * earlier version converges to the corrected shape. Never touches a rule
+         * this adapter has never emitted, including one an operator added by hand.
          */
-        render(config: {
-            root: string;
-            worktreesPath: string;
-        }): Record<string, unknown>;
+        retiredRules(input: PermissionConfigInput): Record<string, unknown>;
+        /** Optional: an additional generated script this harness's config depends on (e.g. a PreToolUse hook). */
+        hookFile?: {
+            /** Filename under templates/hooks/. */
+            templateFileName: string;
+            /** Relative to the store root — where the rendered script is installed. */
+            targetPath: string;
+        };
     };
 }
 /**

package/dist/adapters/types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/adapters/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,MAAM,MAAM,WAAW,GAAG,oBAAoB,GAAG,OAAO,CAAC;AAEzD,MAAM,WAAW,OAAO,CAAC,CAAC,SAAS,WAAW,GAAG,WAAW;IAC1D,IAAI,EAAE,CAAC,CAAC;IACR,EAAE,EAAE,MAAM,CAAC;IACX,gBAAgB,EAAE,MAAM,CAAC;CAC1B;AAED;;;;;GAKG;AACH,eAAO,MAAM,mCAAmC,EAAE,MAAM,CAAC,WAAW,EAAE,MAAM,CAI3E,CAAC;AAEF;;;;;;GAMG;AACH,MAAM,WAAW,wBAAyB,SAAQ,OAAO,CAAC,oBAAoB,CAAC;IAC7E,oGAAoG;IACpG,aAAa,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,YAAY,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACvC,kFAAkF;IAClF,gBAAgB,CAAC,EAAE;QACjB,iEAAiE;QACjE,IAAI,EAAE,MAAM,CAAC;QACb;;;;;;WAMG;QACH,MAAM,CAAC,MAAM,EAAE;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,aAAa,EAAE,MAAM,CAAA;SAAE,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;KAClF,CAAC;CACH;AAED;;;;GAIG;AACH,MAAM,WAAW,cAAc;IAC7B,oBAAoB,EAAE,wBAAwB,CAAC;IAC/C,KAAK,EAAE,OAAO,kBAAkB,EAAE,YAAY,CAAC;CAChD"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/adapters/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,MAAM,MAAM,WAAW,GAAG,oBAAoB,GAAG,OAAO,CAAC;AAEzD,MAAM,WAAW,OAAO,CAAC,CAAC,SAAS,WAAW,GAAG,WAAW;IAC1D,IAAI,EAAE,CAAC,CAAC;IACR,EAAE,EAAE,MAAM,CAAC;IACX,gBAAgB,EAAE,MAAM,CAAC;CAC1B;AAED;;;;;GAKG;AACH,eAAO,MAAM,mCAAmC,EAAE,MAAM,CAAC,WAAW,EAAE,MAAM,CAI3E,CAAC;AAEF;;;;;;GAMG;AACH;;;;;;;;GAQG;AACH,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,EAAE,MAAM,CAAC;IACtB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,wBAAyB,SAAQ,OAAO,CAAC,oBAAoB,CAAC;IAC7E,oGAAoG;IACpG,aAAa,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,YAAY,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACvC,kFAAkF;IAClF,gBAAgB,CAAC,EAAE;QACjB,iEAAiE;QACjE,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,CAAC,KAAK,EAAE,qBAAqB,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QAC9D;;;;;;WAMG;QACH,YAAY,CAAC,KAAK,EAAE,qBAAqB,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QACpE,0GAA0G;QAC1G,QAAQ,CAAC,EAAE;YACT,uCAAuC;YACvC,gBAAgB,EAAE,MAAM,CAAC;YACzB,2EAA2E;YAC3E,UAAU,EAAE,MAAM,CAAC;SACpB,CAAC;KACH,CAAC;CACH;AAED;;;;GAIG;AACH,MAAM,WAAW,cAAc;IAC7B,oBAAoB,EAAE,wBAAwB,CAAC;IAC/C,KAAK,EAAE,OAAO,kBAAkB,EAAE,YAAY,CAAC;CAChD"}

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

@@ -1 +1 @@
-{"version":3,"file":"adapters-generate.d.ts","sourceRoot":"","sources":["../../src/commands/adapters-generate.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAO1E,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAE9C,eAAO,MAAM,QAAQ,EAAE,eAAuC,CAAC;AAE/D,MAAM,WAAW,0BAA0B;IACzC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,0BAA0B,EAAE,CAAC;CACrC;AAMD;;;;;;GAMG;AACH,wDAAwD;AACxD,wBAAsB,sBAAsB,CAAC,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,0BAA0B,EAAE,CAAC,CA4BhG;AAED,wBAAsB,OAAO,CAAC,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,cAAc,CAAC,oBAAoB,CAAC,CAAC,CAWzF"}
+{"version":3,"file":"adapters-generate.d.ts","sourceRoot":"","sources":["../../src/commands/adapters-generate.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAQ1E,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAE9C,eAAO,MAAM,QAAQ,EAAE,eAAuC,CAAC;AAE/D,MAAM,WAAW,0BAA0B;IACzC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,0BAA0B,EAAE,CAAC;CACrC;AAED;;;;;;GAMG;AACH,wDAAwD;AACxD,wBAAsB,sBAAsB,CAAC,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,0BAA0B,EAAE,CAAC,CA2ChG;AAED,wBAAsB,OAAO,CAAC,KAAK,EAAE,KAAK,GAAG,OAAO,CAAC,cAAc,CAAC,oBAAoB,CAAC,CAAC,CAWzF"}

package/dist/commands/adapters-generate.js

@@ -3,12 +3,10 @@ import { configuredAdapters } from '../adapters/registry.js';
 import { agentsMdPath } from '../core/agents-doc.js';
 import { ExitCode } from '../core/exit-codes.js';
 import { upsertFencedRegionInFile } from '../core/fs/fenced-region.js';
+import { installTemplatedHookScript, resolveOwnBinPath } from '../core/hooks.js';
 import { mergeJsonArrayLists } from '../core/json-config-merge.js';
-import { htmlCommentFence } from '../core/markers.js';
+import { harnessEntryFence } from '../core/markers.js';
 export const requires = { store: 'required' };
-function harnessEntryFence(adapterId) {
-    return htmlCommentFence(`adapter:${adapterId}:harness-entry`);
-}
 /**
  * adapters spec / task 8.3-8.4: every configured harness-generation adapter
  * gets its entry file's fenced region (re)written from `render()`, and,
@@ -24,12 +22,23 @@ export async function generateAdapterOutputs(store) {
         const { changed } = await upsertFencedRegionInFile(entryPath, harnessEntryFence(adapter.id), adapter.render(agentsMdPath(store.root)));
         files.push({ path: adapter.entryFileName, changed });
         if (adapter.permissionConfig) {
-            const permPath = path.join(store.root, adapter.permissionConfig.path);
-            const rules = adapter.permissionConfig.render({
+            const input = {
                 root: store.root,
                 worktreesPath: store.config.session.worktrees_path,
+                binPath: resolveOwnBinPath(),
+            };
+            let permChanged = false;
+            if (adapter.permissionConfig.hookFile) {
+                const { changed: hookScriptChanged } = await installTemplatedHookScript(store.root, adapter.permissionConfig.hookFile.targetPath, adapter.permissionConfig.hookFile.templateFileName, { __CONTEXTURE_BIN__: input.binPath });
+                permChanged = permChanged || hookScriptChanged;
+            }
+            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,
             });
-            const { changed: permChanged } = await mergeJsonArrayLists(permPath, rules);
+            permChanged = permChanged || rulesChanged;
             files.push({ path: adapter.permissionConfig.path, changed: permChanged });
         }
     }

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

@@ -1 +1 @@
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package/dist/commands/adapters-write-gate.d.ts

@@ -0,0 +1,20 @@
+import type { RunEnv } from '../core/env.js';
+import { ExitCode } from '../core/exit-codes.js';
+/**
+ * `ctxr adapters write-gate`: the target of the generated Claude Code
+ * PreToolUse hook (claude-code.ts's permissionConfig). This is deliberately
+ * NOT a normal contexture command — it bypasses the --json envelope
+ * entirely and speaks Claude Code's own hook protocol on stdout/exit code,
+ * because that protocol is what the harness parses:
+ *
+ *   - deny: a `permissionDecision: "deny"` JSON body on stdout, exit 0.
+ *   - let normal permission flow apply: exit 0, no output.
+ *   - the gate's own error (unparseable stdin, no resolvable store): a
+ *     nonzero exit that is never 2 — exit 2 hard-blocks the tool call
+ *     regardless of output, and a bug in this gate must never do that; it
+ *     degrades to "normal permission flow applies" instead.
+ */
+export declare function execute(env: RunEnv, flags?: {
+    root?: string;
+}): Promise<ExitCode>;
+//# sourceMappingURL=adapters-write-gate.d.ts.map

package/dist/commands/adapters-write-gate.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"adapters-write-gate.d.ts","sourceRoot":"","sources":["../../src/commands/adapters-write-gate.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAC;AA2BjD;;;;;;;;;;;;;GAaG;AACH,wBAAsB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,GAAE;IAAE,IAAI,CAAC,EAAE,MAAM,CAAA;CAAO,GAAG,OAAO,CAAC,QAAQ,CAAC,CAsD3F"}

package/dist/commands/adapters-write-gate.js

@@ -0,0 +1,77 @@
+import path from 'node:path';
+import { ExitCode } from '../core/exit-codes.js';
+import { openStore } from '../core/store.js';
+import { isWriteInScope } from '../core/write-lifecycle/path-gate.js';
+const GATED_TOOLS = new Set(['Edit', 'Write', 'NotebookEdit']);
+async function readStdin(stream) {
+    const chunks = [];
+    for await (const chunk of stream) {
+        chunks.push(typeof chunk === 'string' ? Buffer.from(chunk) : chunk);
+    }
+    return Buffer.concat(chunks).toString('utf8');
+}
+/**
+ * `ctxr adapters write-gate`: the target of the generated Claude Code
+ * PreToolUse hook (claude-code.ts's permissionConfig). This is deliberately
+ * NOT a normal contexture command — it bypasses the --json envelope
+ * entirely and speaks Claude Code's own hook protocol on stdout/exit code,
+ * because that protocol is what the harness parses:
+ *
+ *   - deny: a `permissionDecision: "deny"` JSON body on stdout, exit 0.
+ *   - let normal permission flow apply: exit 0, no output.
+ *   - the gate's own error (unparseable stdin, no resolvable store): a
+ *     nonzero exit that is never 2 — exit 2 hard-blocks the tool call
+ *     regardless of output, and a bug in this gate must never do that; it
+ *     degrades to "normal permission flow applies" instead.
+ */
+export async function execute(env, flags = {}) {
+    let raw;
+    try {
+        raw = await readStdin(env.io.stdin);
+    }
+    catch {
+        return ExitCode.Internal;
+    }
+    let input;
+    try {
+        input = JSON.parse(raw);
+    }
+    catch {
+        return ExitCode.Internal;
+    }
+    const toolName = input.tool_name;
+    if (!toolName || !GATED_TOOLS.has(toolName)) {
+        return ExitCode.Ok;
+    }
+    const targetPath = input.tool_input?.file_path ?? input.tool_input?.notebook_path;
+    if (!targetPath) {
+        return ExitCode.Ok;
+    }
+    const cwd = input.cwd ?? env.cwd;
+    const effectiveEnv = cwd === env.cwd ? env : { ...env, cwd };
+    let root;
+    let config;
+    try {
+        ({ root, config } = await openStore(effectiveEnv, flags));
+    }
+    catch {
+        return ExitCode.Internal;
+    }
+    const relativePath = path.relative(root, path.resolve(cwd, targetPath));
+    const scope = await isWriteInScope(config, root, relativePath);
+    if (scope.inScope) {
+        return ExitCode.Ok;
+    }
+    const reason = `contexture: "${targetPath}" ${scope.reason ?? 'is outside the active session worktree'} in the store at "${root}". ` +
+        'Run "ctxr session start" and make this edit inside its worktree instead.';
+    const decision = {
+        hookSpecificOutput: {
+            hookEventName: 'PreToolUse',
+            permissionDecision: 'deny',
+            permissionDecisionReason: reason,
+        },
+    };
+    env.io.stdout.write(`${JSON.stringify(decision)}\n`);
+    return ExitCode.Ok;
+}
+//# sourceMappingURL=adapters-write-gate.js.map

package/dist/commands/adapters-write-gate.js.map

@@ -0,0 +1 @@
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package/dist/commands/init.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAyB1E,OAAO,EAAmE,KAAK,mBAAmB,EAAE,MAAM,qBAAqB,CAAC;AAYhI,OAAO,EAAiB,KAAK,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAgB5D,eAAO,MAAM,QAAQ,EAAE,eAAqC,CAAC;AAE7D,MAAM,WAAW,SAAS;IACxB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,mBAAmB,EAAE,OAAO,CAAC;IAC7B,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,GAAG,EAAE;QAAE,kBAAkB,EAAE,OAAO,CAAC;QAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAA;KAAE,CAAC;IAC3F,wFAAwF;IACxF,QAAQ,EAAE;QAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,MAAM,EAAE,mBAAmB,EAAE,CAAA;KAAE,CAAC;IACpE,cAAc,EAAE,MAAM,CAAC;CACxB;AAqMD,wBAAsB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,GAAG,OAAO,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAY9F"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AA0B1E,OAAO,EAAmE,KAAK,mBAAmB,EAAE,MAAM,qBAAqB,CAAC;AAYhI,OAAO,EAAiB,KAAK,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAgB5D,eAAO,MAAM,QAAQ,EAAE,eAAqC,CAAC;AAE7D,MAAM,WAAW,SAAS;IACxB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,mBAAmB,EAAE,OAAO,CAAC;IAC7B,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,GAAG,EAAE;QAAE,kBAAkB,EAAE,OAAO,CAAC;QAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAA;KAAE,CAAC;IAC3F,wFAAwF;IACxF,QAAQ,EAAE;QAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,MAAM,EAAE,mBAAmB,EAAE,CAAA;KAAE,CAAC;IACpE,cAAc,EAAE,MAAM,CAAC;CACxB;AAqMD,wBAAsB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,GAAG,OAAO,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAY9F"}

package/dist/commands/init.js

@@ -3,12 +3,12 @@ import { mkdir, readFile } from 'node:fs/promises';
 import path from 'node:path';
 import { parse as parseYaml } from 'yaml';
 import { z } from 'zod';
-import { DEFAULT_ADAPTERS, DEFAULT_ARCHIVE_PATH, DEFAULT_ROLLUP_STALE_DAYS, DEFAULT_CATALOG_PATH, DEFAULT_CATALOG_SECTION_MAX_BYTES, DEFAULT_CONVENTIONS_PATH, DEFAULT_DERIVED_PATHS, DEFAULT_DIFF_SIZE_CEILING_LINES, DEFAULT_EXCLUDE_PATHS, DEFAULT_HARD_WALLS, DEFAULT_INBOX_PATH, DEFAULT_TRACKING_PARAMS, DEFAULT_INTERNAL_AUDIENCES, DEFAULT_PROCEDURES_PATH, DEFAULT_RELATIONS, DEFAULT_GRAPH_SETTINGS, DEFAULT_SESSION_BRANCH_PREFIX, DEFAULT_VISIBILITY_CONTEXT, DEFAULT_VISIBILITY_FIELD_KEY, DEFAULT_WORKTREES_PATH, } from '../config/defaults.js';
+import { DEFAULT_ADAPTERS, DEFAULT_ARCHIVE_PATH, DEFAULT_ROLLUP_STALE_DAYS, DEFAULT_CATALOG_PATH, DEFAULT_CATALOG_SECTION_MAX_BYTES, DEFAULT_CONVENTIONS_PATH, DEFAULT_DERIVED_PATHS, DEFAULT_DIFF_SIZE_CEILING_LINES, DEFAULT_EXCLUDE_PATHS, DEFAULT_HARD_WALLS, DEFAULT_INBOX_PATH, DEFAULT_TRACKING_PARAMS, DEFAULT_INTERNAL_AUDIENCES, DEFAULT_SKILLS_PATH, DEFAULT_RELATIONS, DEFAULT_GRAPH_SETTINGS, DEFAULT_SESSION_BRANCH_PREFIX, DEFAULT_VISIBILITY_CONTEXT, DEFAULT_VISIBILITY_FIELD_KEY, DEFAULT_WORKSPACES_EXTERNAL, DEFAULT_WORKTREES_PATH, } from '../config/defaults.js';
 import { configPathFor, readConfig } from '../config/load.js';
 import { renderStoreConfig } from '../config/render.js';
 import { SUPPORTED_SCHEMA_VERSION, TaxonomyLayerSchema } from '../config/schema.js';
 import { buildAgentsCanonicalSection, buildAgentsCaptureSection, buildAgentsConventionsSection, buildAgentsLegRoutingSection, buildAgentsPlacementSection, agentsMdPath, } from '../core/agents-doc.js';
-import { syncShippedSkills } from '../core/procedures.js';
+import { syncShippedSkills } from '../core/skills.js';
 import { reconcileStore, WORKTREES_GITIGNORE_FENCE } from '../core/reconcile.js';
 import { isInteractive } from '../core/env.js';
 import { GitIdentityMissingError, InvalidTaxonomyFileError, TaxonomySelectionConflictError, UnknownTaxonomyProfileError, } from '../core/errors.js';
@@ -127,13 +127,13 @@ async function runInitCore(env, flags) {
         derived: { paths: [...DEFAULT_DERIVED_PATHS] },
         retrieval: { exclude_paths: [...DEFAULT_EXCLUDE_PATHS], relations: [...DEFAULT_RELATIONS], graph: { ...DEFAULT_GRAPH_SETTINGS, orphan_exempt_clusters: [] } },
         git: { default_branch: defaultBranch },
-        session: { branch_prefix: DEFAULT_SESSION_BRANCH_PREFIX, worktrees_path: DEFAULT_WORKTREES_PATH },
+        session: { branch_prefix: DEFAULT_SESSION_BRANCH_PREFIX, worktrees_path: DEFAULT_WORKTREES_PATH, workspaces_external: DEFAULT_WORKSPACES_EXTERNAL },
         write_lifecycle: { diff_size_ceiling_lines: DEFAULT_DIFF_SIZE_CEILING_LINES, writable_paths: [] },
         catalog: { path: DEFAULT_CATALOG_PATH, section_max_bytes: DEFAULT_CATALOG_SECTION_MAX_BYTES },
         disclosure: { internal_audiences: [...DEFAULT_INTERNAL_AUDIENCES], hard_walls: [...DEFAULT_HARD_WALLS], leak_markers: {} },
         ingest: { inbox_path: DEFAULT_INBOX_PATH, tracking_params: [...DEFAULT_TRACKING_PARAMS] },
         organize: { archive_path: DEFAULT_ARCHIVE_PATH, rollup_stale_days: DEFAULT_ROLLUP_STALE_DAYS },
-        harness: { procedures_path: DEFAULT_PROCEDURES_PATH, conventions_path: DEFAULT_CONVENTIONS_PATH },
+        harness: { skills_path: DEFAULT_SKILLS_PATH, conventions_path: DEFAULT_CONVENTIONS_PATH },
         adapters: [...DEFAULT_ADAPTERS],
     };
     // Round-trips through the schema internally; throws before any byte is written if it doesn't.
@@ -145,7 +145,7 @@ async function runInitCore(env, flags) {
     await buildAgentsLegRoutingSection(root, config);
     await buildAgentsCaptureSection(root, config);
     await buildAgentsPlacementSection(root, config);
-    const procedureFilesCreated = await syncShippedSkills(root, config);
+    const skillFilesCreated = await syncShippedSkills(root, config);
     await buildAgentsCanonicalSection(root, config);
     await buildAgentsConventionsSection(root, config);
     // One directory per configured layer with a .gitkeep — makes Zettelkasten's
@@ -165,13 +165,13 @@ async function runInitCore(env, flags) {
     const { changed: hookFiles } = await installHooks(root, defaultBranch);
     await configureHooksPath(env.git, root);
     const relConfigPath = path.relative(root, configPath);
-    await addPaths(env.git, root, [relConfigPath, '.gitignore', path.relative(root, agentsMdPath(root)), ...layerGitkeeps, ...procedureFilesCreated, ...hookFiles]);
+    await addPaths(env.git, root, [relConfigPath, '.gitignore', path.relative(root, agentsMdPath(root)), ...layerGitkeeps, ...skillFilesCreated, ...hookFiles]);
     const commitSha = await commitIfStaged(env.git, root, { kind: 'bootstrap' }, 'chore: initialize contexture store');
     return {
         data: {
             root,
             already_initialized: false,
-            created: [relConfigPath, '.gitignore', path.relative(root, agentsMdPath(root)), ...layerGitkeeps, ...procedureFilesCreated, ...hookFiles],
+            created: [relConfigPath, '.gitignore', path.relative(root, agentsMdPath(root)), ...layerGitkeeps, ...skillFilesCreated, ...hookFiles],
             unchanged: [],
             git: { repository_created: !repositoryAlreadyExists, commit: commitSha, default_branch: defaultBranch },
             taxonomy: {

package/dist/commands/init.js.map

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package/dist/commands/rollup-stale.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"rollup-stale.d.ts","sourceRoot":"","sources":["../../src/commands/rollup-stale.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAC1E,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAI7C,OAAO,EAAoB,KAAK,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAC5E,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAE9C,eAAO,MAAM,QAAQ,EAAE,eAAuC,CAAC;AAE/D,MAAM,WAAW,gBAAgB;IAC/B,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,gBAAgB,EAAE,CAAC;CAC3B;AAOD;;;;GAIG;AACH,wBAAsB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,gBAAgB,GAAG,OAAO,CAAC,cAAc,CAAC,eAAe,CAAC,CAAC,CAkB1H"}
+{"version":3,"file":"rollup-stale.d.ts","sourceRoot":"","sources":["../../src/commands/rollup-stale.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AAC1E,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAI7C,OAAO,EAAoB,KAAK,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAC5E,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAE9C,eAAO,MAAM,QAAQ,EAAE,eAAuC,CAAC;AAE/D,MAAM,WAAW,gBAAgB;IAC/B,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,gBAAgB,EAAE,CAAC;CAC3B;AAOD;;;;GAIG;AACH,wBAAsB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,gBAAgB,GAAG,OAAO,CAAC,cAAc,CAAC,eAAe,CAAC,CAAC,CAyB1H"}

package/dist/commands/rollup-stale.js

@@ -22,7 +22,7 @@ export async function execute(env, store, flags) {
             throw new NoteNotFoundError(entity);
     }
     const notes = await listNotes(store.root, store.config);
-    const stale = await findStaleRollups(env.git, store.root, notes, { entity }, store.config.organize.rollup_stale_days);
+    const stale = await findStaleRollups(env.git, store.root, notes, { entity, missionPath: store.config.organize.mission_path }, store.config.organize.rollup_stale_days, env.now());
     return {
         exitCode: ExitCode.Ok,
         data: { stale },

package/dist/commands/rollup-stale.js.map

@@ -1 +1 @@
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