ctxr-cli 0.20.0 → 0.21.0

package/dist/core/ingest/required-sections.d.ts

@@ -2,9 +2,9 @@ import type { StoreConfig } from '../../config/schema.js';
 /**
  * context-ingest spec: the section a capture of this source type must carry
  * for ingest to accept it as provenance, when the store has declared one and
- * the capture does not have it. `undefined` means nothing is owed — either
- * the store declared no section for this source type, or the capture carries
- * the one it declared.
+ * the capture does not have it, or has it with nothing under it. `undefined`
+ * means nothing is owed — either the store declared no section for this source
+ * type, or the capture carries the one it declared.
  *
  * The body passed here is the markdown the capture presents. For material
  * that is not markdown that is the sidecar's body, which needs no special

package/dist/core/ingest/required-sections.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"required-sections.d.ts","sourceRoot":"","sources":["../../../src/core/ingest/required-sections.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAyB1D;;;;;;;;;;;GAWG;AACH,wBAAgB,sBAAsB,CACpC,MAAM,EAAE,IAAI,CAAC,WAAW,EAAE,QAAQ,CAAC,EACnC,UAAU,EAAE,MAAM,GAAG,SAAS,EAC9B,IAAI,EAAE,MAAM,GACX,MAAM,GAAG,SAAS,CAIpB"}
+{"version":3,"file":"required-sections.d.ts","sourceRoot":"","sources":["../../../src/core/ingest/required-sections.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AA6F1D;;;;;;;;;;;GAWG;AACH,wBAAgB,sBAAsB,CACpC,MAAM,EAAE,IAAI,CAAC,WAAW,EAAE,QAAQ,CAAC,EACnC,UAAU,EAAE,MAAM,GAAG,SAAS,EAC9B,IAAI,EAAE,MAAM,GACX,MAAM,GAAG,SAAS,CAIpB"}

package/dist/core/ingest/required-sections.js

@@ -1,31 +1,94 @@
 /**
- * Any ATX heading, at any level. Level-agnostic deliberately
- * (capture-is-an-owned-skill design D6): a capture carries its source's
- * markdown as the source wrote it, so a `## Summary` section may hold
- * `#`-level headings of its own. Pinning the declared section to one level
- * would make a store's configuration depend on structure the capture
- * procedure explicitly refuses to normalize.
+ * An ATX heading: up to three spaces of indent, one to six `#`, then text.
+ * Level-agnostic for MATCHING deliberately (capture-is-an-owned-skill design
+ * D6): a capture carries its source's markdown as the source wrote it, so a
+ * `## Summary` section may hold `#`-level headings of its own. Pinning the
+ * declared section to one level would make a store's configuration depend on
+ * structure the capture procedure explicitly refuses to normalize. The level
+ * is used for one thing only: knowing where a section ends.
  */
-const HEADING_RE = /^#{1,6}\s+(.+)$/gm;
+const HEADING_RE = /^ {0,3}(#{1,6})\s+(.+?)\s*$/;
+/** A code fence's opening or closing line: three or more backticks or tildes. */
+const FENCE_RE = /^ {0,3}(`{3,}|~{3,})(.*)$/;
 /**
+ * Splits a body into lines tagged with whether markdown would treat them as
+ * code. A fence opens on three or more backticks or tildes and closes on the
+ * same character at least as long with nothing after it; a backtick fence's
+ * info string may not itself contain a backtick (that is inline code, not a
+ * fence); an unclosed fence runs to the end of the file, as markdown does.
+ */
+function tagLines(body) {
+    const lines = [];
+    let open;
+    for (const text of body.split(/\r?\n/)) {
+        const fence = FENCE_RE.exec(text);
+        if (open !== undefined) {
+            const closes = fence !== null && fence[1][0] === open.char && fence[1].length >= open.length && fence[2].trim() === '';
+            lines.push({ text, fenced: true, fenceMarker: closes });
+            if (closes)
+                open = undefined;
+            continue;
+        }
+        const opens = fence !== null && !(fence[1][0] === '`' && fence[2].includes('`'));
+        if (opens)
+            open = { char: fence[1][0], length: fence[1].length };
+        lines.push({ text, fenced: opens, fenceMarker: opens });
+    }
+    return lines;
+}
+/**
+ * Whether the capture carries `section` with something under it.
+ *
  * Matching is case-sensitive, unlike `headingsOf` in the integrity checks,
  * which lowercases because it is looking for accidental duplication between
  * two documents. Here the declared name is a store's own statement of what a
  * capture of that type must carry, and a capture that answers it in different
  * case has not answered it — being told so is more useful than a silent pass.
+ *
+ * harden-the-required-capture-section D1: a heading only counts outside a
+ * fenced code block (a `## Transcript` in a document about markup is a string,
+ * not a section), and a section is the heading plus the lines up to the next
+ * heading of the same or a shallower level, or the end of the file. It holds
+ * something if at least one of those lines is non-blank and is neither a
+ * heading nor a fence's own opening or closing line. Text INSIDE a fenced block
+ * counts: a transcript pasted into a code block is still a transcript. This is
+ * still shape and says nothing about whether the record is complete.
  */
-function headingTexts(body) {
-    const headings = new Set();
-    for (const match of body.matchAll(HEADING_RE))
-        headings.add(match[1].trim());
-    return headings;
+function carriesSectionWithContent(body, section) {
+    const lines = tagLines(body);
+    const headingAt = (i) => {
+        const line = lines[i];
+        if (line.fenced)
+            return undefined;
+        const match = HEADING_RE.exec(line.text);
+        return match === null ? undefined : { level: match[1].length, text: match[2] };
+    };
+    for (let i = 0; i < lines.length; i++) {
+        const heading = headingAt(i);
+        if (heading === undefined || heading.text !== section)
+            continue;
+        for (let j = i + 1; j < lines.length; j++) {
+            const next = headingAt(j);
+            if (next !== undefined) {
+                if (next.level <= heading.level)
+                    break;
+                continue; // a deeper heading is part of this section, but is not content in itself
+            }
+            const line = lines[j];
+            if (line.fenceMarker)
+                continue;
+            if (line.text.trim() !== '')
+                return true;
+        }
+    }
+    return false;
 }
 /**
  * context-ingest spec: the section a capture of this source type must carry
  * for ingest to accept it as provenance, when the store has declared one and
- * the capture does not have it. `undefined` means nothing is owed — either
- * the store declared no section for this source type, or the capture carries
- * the one it declared.
+ * the capture does not have it, or has it with nothing under it. `undefined`
+ * means nothing is owed — either the store declared no section for this source
+ * type, or the capture carries the one it declared.
  *
  * The body passed here is the markdown the capture presents. For material
  * that is not markdown that is the sidecar's body, which needs no special
@@ -36,6 +99,6 @@ export function missingRequiredSection(config, sourceType, body) {
     const declared = sourceType === undefined ? undefined : config.ingest.required_capture_sections?.[sourceType];
     if (declared === undefined)
         return undefined;
-    return headingTexts(body).has(declared) ? undefined : declared;
+    return carriesSectionWithContent(body, declared) ? undefined : declared;
 }
 //# sourceMappingURL=required-sections.js.map

package/dist/core/ingest/required-sections.js.map

@@ -1 +1 @@
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+{"version":3,"file":"required-sections.js","sourceRoot":"","sources":["../../../src/core/ingest/required-sections.ts"],"names":[],"mappings":"AAEA;;;;;;;;GAQG;AACH,MAAM,UAAU,GAAG,6BAA6B,CAAC;AAEjD,iFAAiF;AACjF,MAAM,QAAQ,GAAG,2BAA2B,CAAC;AAU7C;;;;;;GAMG;AACH,SAAS,QAAQ,CAAC,IAAY;IAC5B,MAAM,KAAK,GAAW,EAAE,CAAC;IACzB,IAAI,IAAkD,CAAC;IACvD,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAClC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,MAAM,MAAM,GAAG,KAAK,KAAK,IAAI,IAAI,KAAK,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,IAAI,IAAI,KAAK,CAAC,CAAC,CAAE,CAAC,MAAM,IAAI,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,KAAK,EAAE,CAAC;YAC1H,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,CAAC,CAAC;YACxD,IAAI,MAAM;gBAAE,IAAI,GAAG,SAAS,CAAC;YAC7B,SAAS;QACX,CAAC;QACD,MAAM,KAAK,GAAG,KAAK,KAAK,IAAI,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,KAAK,CAAC,CAAC,CAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;QACnF,IAAI,KAAK;YAAE,IAAI,GAAG,EAAE,IAAI,EAAE,KAAM,CAAC,CAAC,CAAE,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,KAAM,CAAC,CAAC,CAAE,CAAC,MAAM,EAAE,CAAC;QACtE,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,KAAK,EAAE,CAAC,CAAC;IAC1D,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,SAAS,yBAAyB,CAAC,IAAY,EAAE,OAAe;IAC9D,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC;IAC7B,MAAM,SAAS,GAAG,CAAC,CAAS,EAA+C,EAAE;QAC3E,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAC;QACvB,IAAI,IAAI,CAAC,MAAM;YAAE,OAAO,SAAS,CAAC;QAClC,MAAM,KAAK,GAAG,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACzC,OAAO,KAAK,KAAK,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC,CAAE,EAAE,CAAC;IACnF,CAAC,CAAC;IAEF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,MAAM,OAAO,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC;QAC7B,IAAI,OAAO,KAAK,SAAS,IAAI,OAAO,CAAC,IAAI,KAAK,OAAO;YAAE,SAAS;QAChE,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC1C,MAAM,IAAI,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC;YAC1B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,IAAI,IAAI,CAAC,KAAK,IAAI,OAAO,CAAC,KAAK;oBAAE,MAAM;gBACvC,SAAS,CAAC,yEAAyE;YACrF,CAAC;YACD,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAC;YACvB,IAAI,IAAI,CAAC,WAAW;gBAAE,SAAS;YAC/B,IAAI,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,KAAK,EAAE;gBAAE,OAAO,IAAI,CAAC;QAC3C,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,sBAAsB,CACpC,MAAmC,EACnC,UAA8B,EAC9B,IAAY;IAEZ,MAAM,QAAQ,GAAG,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,yBAAyB,EAAE,CAAC,UAAU,CAAC,CAAC;IAC9G,IAAI,QAAQ,KAAK,SAAS;QAAE,OAAO,SAAS,CAAC;IAC7C,OAAO,yBAAyB,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC;AAC1E,CAAC"}

package/dist/core/notes/list.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../../src/core/notes/list.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAI1D,+DAA+D;AAC/D,MAAM,WAAW,SAAS;IACxB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,IAAI;IACnB,gEAAgE;IAChE,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,SAAS,CAAC;IACjD,IAAI,EAAE,MAAM,CAAC;CACd;AAmCD;;;;;GAKG;AACH,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AAEnD,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,EAAE,CAiBjE;AAkCD;;;;;;;;;;;GAWG;AACH,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,CAM1F;AAED,wGAAwG;AACxG,wBAAsB,SAAS,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,KAAK,GAAE,SAAc,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,CAO9G"}
+{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../../src/core/notes/list.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAI1D,+DAA+D;AAC/D,MAAM,WAAW,SAAS;IACxB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,IAAI;IACnB,gEAAgE;IAChE,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,SAAS,CAAC;IACjD,IAAI,EAAE,MAAM,CAAC;CACd;AAmCD;;;;;GAKG;AACH,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AAEnD,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,WAAW,GAAG,MAAM,EAAE,CAmBjE;AAkCD;;;;;;;;;;;GAWG;AACH,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,CAM1F;AAED,wGAAwG;AACxG,wBAAsB,SAAS,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,KAAK,GAAE,SAAc,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,CAO9G"}

package/dist/core/notes/list.js

@@ -1,3 +1,4 @@
+import { DEFAULT_LOG_PATH } from '../../config/defaults.js';
 import { readdir } from 'node:fs/promises';
 import path from 'node:path';
 import { configuredAdapters } from '../../adapters/registry.js';
@@ -55,6 +56,8 @@ export function excludedPrefixesFor(config) {
         // than relying on the default path sitting inside `.contexture/`, so the
         // exclusion follows a store that configures the path elsewhere.
         config.templates.path,
+        // standardize-store-operating-guidance: the store log records what happened, never a note.
+        config.organize.log_path ?? DEFAULT_LOG_PATH,
     ];
 }
 async function walk(dir, root, excludePrefixes, skipRootFiles, results) {

package/dist/core/notes/list.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;AAYvC,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,CA4E7G"}

package/dist/core/reconcile.js

@@ -1,7 +1,8 @@
 import path from 'node:path';
 import { DEFAULT_BASELINE_CONVENTIONS_FILE_NAME } from '../config/defaults.js';
 import { CLI_VERSION } from '../version.js';
-import { agentsMdPath, AGENTS_MD_SECTION_ORDER, buildAgentsCanonicalSection, buildAgentsCaptureSection, buildAgentsConventionsSection, buildAgentsLegRoutingSection, buildAgentsMissionSection, buildAgentsPlacementSection, } from './agents-doc.js';
+import { generateAdapterOutputs } from './adapter-outputs.js';
+import { agentsMdPath, AGENTS_MD_SECTION_ORDER, buildAgentsCanonicalSection, buildAgentsCaptureSection, buildAgentsConventionsSection, buildAgentsGuidanceIndexSection, buildAgentsLegRoutingSection, buildAgentsMissionSection, buildAgentsPlacementSection, } from './agents-doc.js';
 import { removeManagedBaselineFile } from './convention-doc.js';
 import { removeFencedRegionFromFile, reorderFencedRegionsInFile, upsertFencedRegionInFile } from './fs/fenced-region.js';
 import { bridgeHarnessSkills } from './harness/bridge.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.
@@ -80,6 +82,7 @@ export async function reconcileStore(env, root, config) {
         buildAgentsCanonicalSection,
         buildAgentsMissionSection,
         buildAgentsConventionsSection,
+        buildAgentsGuidanceIndexSection,
     ]) {
         if ((await build(root, config)).changed)
             agentsChanged = true;
@@ -95,6 +98,11 @@ 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

@@ -3,7 +3,7 @@ import { readdirSync, readFileSync } from 'node:fs';
 import { mkdir, readdir, readFile, rm } from 'node:fs/promises';
 import path from 'node:path';
 import { fileURLToPath } from 'node:url';
-import { DEFAULT_HOUSE_CONVENTIONS_FILE_NAME, RELATION_DIRECTEDNESS_NOTE, RELATION_VOCABULARY } from '../config/defaults.js';
+import { DEFAULT_HOUSE_CONVENTIONS_FILE_NAME, DEFAULT_LOG_PATH, DEFAULT_MISSION_MAX_BYTES, RELATION_DIRECTEDNESS_NOTE, RELATION_VOCABULARY } from '../config/defaults.js';
 import { scanDocsDir, SKILL_FILE_NAME } from './conventions.js';
 import { GRAPH_DOCUMENT_RELATIVE_PATH } from './graph/persist.js';
 import { writeFileAtomic } from './fs/atomic.js';
@@ -111,6 +111,7 @@ const PLACEMENT = {
     body: (config) => skillTemplate('ctxr-placement')
         .replace('__LAYER_STEP__', placementLayerStep(config).join('\n'))
         .replaceAll('__TEMPLATES_PATH__', config.templates.path)
+        .replaceAll('__CLUSTER_DEPTH__', String(config.retrieval.graph.cluster_depth))
         .split('\n'),
 };
 /**
@@ -125,7 +126,10 @@ 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',
@@ -134,6 +138,7 @@ const INGEST_ORCHESTRATION = {
     body: (config) => skillTemplate('ctxr-ingest-orchestration')
         .replaceAll('__GRAPH_DOCUMENT_PATH__', GRAPH_DOCUMENT_RELATIVE_PATH)
         .replaceAll('__TEMPLATES_PATH__', config.templates.path)
+        .replaceAll('__LOG_PATH__', config.organize.log_path ?? DEFAULT_LOG_PATH)
         .split('\n'),
 };
 const CONNECTION_FINDING = {
@@ -179,8 +184,11 @@ const ROLLUP = {
 const MISSION = {
     file: 'ctxr-mission',
     name: 'Mission',
-    description: "Keep the store's mission document current from recent work and its taxonomy layers, with every active priority naming its status/purpose/next action, back-burner items stating why they're dormant, and sunset candidates and debt carried as their own sections.",
-    body: () => skillTemplate('ctxr-mission').split('\n'),
+    description: "Keep the store's mission core current — the primary mission, the top priorities in rank order with status/purpose/next action, and what is not now — with the back burner, sunset candidates, and open debt in a linked register; propose changes and write only on the operator's confirmation.",
+    body: (config) => skillTemplate('ctxr-mission')
+        .replaceAll('__LOG_PATH__', config.organize.log_path ?? DEFAULT_LOG_PATH)
+        .replaceAll('__MISSION_MAX_BYTES__', String(config.organize.mission_max_bytes ?? DEFAULT_MISSION_MAX_BYTES))
+        .split('\n'),
 };
 const SUBMIT = {
     file: 'ctxr-submit',
@@ -232,7 +240,10 @@ const ORGANIZE_AUDIT = {
     file: 'ctxr-organize-audit',
     name: 'Organize audit',
     description: 'Audit store health with ctxr lint (observations) and ctxr doctor (blocking invariants), retire by moving, and classify broken links before fixing them.',
-    body: () => skillTemplate('ctxr-organize-audit').split('\n'),
+    body: (config) => skillTemplate('ctxr-organize-audit')
+        .replaceAll('__LOG_PATH__', config.organize.log_path ?? DEFAULT_LOG_PATH)
+        .replaceAll('__ARCHIVE_DESTINATION__', config.organize.archive_destination)
+        .split('\n'),
 };
 const PUBLISH = {
     file: 'ctxr-publish',

package/dist/core/skills.js.map

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package/dist/run.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../src/run.ts"],"names":[],"mappings":"AA+BA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,eAAe,CAAC;AAE5C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAQhD;;;;;GAKG;AACH,eAAO,MAAM,aAAa,YAAI,MAAM,EAAE,QAAQ,EAAE,SAAS,CAAU,CAAC;AAuIpE,wBAAsB,GAAG,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,EAAE,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAmiBjF"}
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../src/run.ts"],"names":[],"mappings":"AAgCA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,eAAe,CAAC;AAE5C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAQhD;;;;;GAKG;AACH,eAAO,MAAM,aAAa,YAAI,MAAM,EAAE,QAAQ,EAAE,SAAS,CAAU,CAAC;AAuIpE,wBAAsB,GAAG,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,EAAE,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAgjBjF"}

package/dist/run.js

@@ -14,6 +14,7 @@ import * as graphQueryCommand from './commands/graph-query.js';
 import * as initCommand from './commands/init.js';
 import * as publishGatherCommand from './commands/publish-gather.js';
 import * as publishCheckCommand from './commands/publish-check.js';
+import * as publishUrlsCommand from './commands/publish-urls.js';
 import * as publishNewCommand from './commands/publish-new.js';
 import * as sessionCaptureCommand from './commands/session-capture.js';
 import * as sessionListCommand from './commands/session-list.js';
@@ -179,7 +180,7 @@ export async function run(argv, env) {
         .description('create a new context store, or reconcile an existing one')
         .option('--profile <id>', 'shipped taxonomy profile id (para, zettelkasten, diataxis)')
         .option('--taxonomy <path>', 'path to a custom taxonomy definition file')
-        .option('--harness <ids>', 'comma-separated harness-generation adapters to target (claude-code, hermes-agent), or "none"')
+        .option('--harness <ids>', `comma-separated harness-generation adapters to target (${initCommand.SELECTABLE_HARNESS_IDS.join(', ')}), or "none"`)
         .action(async (cmdOpts, cmd) => {
         const { runEnv, jsonMode, root } = deriveRunEnv(env, cmd);
         result = await runCommand('init', runEnv, jsonMode, () => initCommand.execute(runEnv, { root, profile: cmdOpts.profile, taxonomy: cmdOpts.taxonomy, harness: cmdOpts.harness }));
@@ -516,6 +517,18 @@ export async function run(argv, env) {
             return publishCheckCommand.execute(store, { path: pagePath });
         });
     });
+    publishCommand
+        .command('urls')
+        .description('the addresses of every page a change set adds, modifies, moves or removes — the staged changes (--staged) or everything since a ref (--since) — for a pull request body to carry')
+        .option('--staged', 'the staged changes')
+        .option('--since <ref>', 'the changes since this ref, as a pull request against it would show')
+        .action(async (cmdOpts, cmd) => {
+        const { runEnv, jsonMode, root } = deriveRunEnv(env, cmd);
+        result = await runCommand('publish.urls', runEnv, jsonMode, async () => {
+            const store = await openStore(runEnv, { root });
+            return publishUrlsCommand.execute(store, { staged: cmdOpts.staged === true, since: cmdOpts.since });
+        });
+    });
     const adaptersCommand = program.command('adapters').description('harness-generation and forge adapters');
     adaptersCommand
         .command('generate')