fix(ci): repair holmes comment template indentation

.github/actions/run-holmes-command/action.yml

@@ -0,0 +1,64 @@
+name: Run HOLMES CLI
+description: Execute Wesley HOLMES CLI reporting command and collect artifacts.
+inputs:
+  command:
+    description: HOLMES CLI subcommand to execute (investigate|verify|predict)
+    required: true
+  report-name:
+    description: Base name for report files (holmes|watson|moriarty)
+    required: true
+  schema-path:
+    description: Path to the GraphQL schema relative to the repository root
+    required: true
+  bundle-dir:
+    description: Path to the Wesley bundle directory relative to the repository root
+    required: true
+  history-file:
+    description: Path to MORIARTY history JSON relative to the repository root (defaults to <bundle-dir>/history.json)
+    required: false
+runs:
+  using: composite
+  steps:
+    - shell: bash
+      run: |
+        set -euo pipefail
+        command="${{ inputs.command }}"
+        report="${{ inputs['report-name'] }}"
+        schema_rel="${{ inputs['schema-path'] }}"
+        bundle_rel="${{ inputs['bundle-dir'] }}"
+        history_rel="${{ inputs['history-file'] }}"
+
+        schema_path="$GITHUB_WORKSPACE/$schema_rel"
+        if [ ! -f "$schema_path" ]; then
+          echo "Schema file not found at $schema_path" >&2
+          exit 1
+        fi
+
+        schema_dir="$(dirname "$schema_path")"
+        bundle_dir="$GITHUB_WORKSPACE/$bundle_rel"
+        bundle_json="$bundle_dir/bundle.json"
+        if [ ! -f "$bundle_json" ]; then
+          echo "Wesley bundle not found at $bundle_json" >&2
+          exit 1
+        fi
+
+        if [ -n "$history_rel" ]; then
+          history_path="$GITHUB_WORKSPACE/$history_rel"
+        else
+          history_path="$bundle_dir/history.json"
+        fi
+
+        json_path="$schema_dir/${report}-report.json"
+        md_path="$schema_dir/${report}-report.md"
+
+        node "$GITHUB_WORKSPACE/packages/wesley-holmes/src/cli.mjs" "$command" \
+          --bundle-dir "$bundle_dir" \
+          --history-file "$history_path" \
+          --json "$json_path" > "$md_path"
+
+        cat "$md_path"
+
+        reports_dir="$GITHUB_WORKSPACE/reports/$report"
+        mkdir -p "$reports_dir"
+        cp "$json_path" "$reports_dir/${report}-report.json"
+        cp "$md_path" "$reports_dir/${report}-report.md"

.github/workflows/wesley-holmes.yml

@@ -42,6 +42,13 @@ jobs:
           else
             echo "No scores.json found yet"
           fi
+
+      - name: "📤 Upload Dashboard Template"
+        uses: actions/upload-artifact@v4
+        with:
+          name: dashboard-template
+          path: docs/holmes-dashboard
+          if-no-files-found: error
 
       - name: "📦 Prepare Bundle for Upload"
         run: |
@@ -78,17 +85,13 @@ jobs:
 
       - name: "🔍 Run Investigation"
         id: holmes
-        run: |
-          set -euo pipefail
-          SCHEMA_DIR="$(dirname "${HOLMES_SCHEMA}")"
-          pushd "$SCHEMA_DIR" >/dev/null
-          node ../packages/wesley-holmes/src/cli.mjs investigate --json holmes-report.json > holmes-report.md
-          cat holmes-report.md
-          popd >/dev/null
-          mkdir -p reports/holmes
-          cp "$SCHEMA_DIR/holmes-report.md" reports/holmes/holmes-report.md
-          cp "$SCHEMA_DIR/holmes-report.json" reports/holmes/holmes-report.json
-
+        uses: ./.github/actions/run-holmes-command
+        with:
+          command: investigate
+          report-name: holmes
+          schema-path: ${{ env.HOLMES_SCHEMA }}
+          bundle-dir: ${{ env.HOLMES_BUNDLE_DIR }}
+
       - name: "💾 Save Report"
         uses: actions/upload-artifact@v4
         with:
@@ -116,17 +119,13 @@ jobs:
 
       - name: "🩺 Run Verification"
         id: watson
-        run: |
-          set -euo pipefail
-          SCHEMA_DIR="$(dirname "${HOLMES_SCHEMA}")"
-          pushd "$SCHEMA_DIR" >/dev/null
-          node ../packages/wesley-holmes/src/cli.mjs verify --json watson-report.json > watson-report.md
-          cat watson-report.md
-          popd >/dev/null
-          mkdir -p reports/watson
-          cp "$SCHEMA_DIR/watson-report.md" reports/watson/watson-report.md
-          cp "$SCHEMA_DIR/watson-report.json" reports/watson/watson-report.json
-
+        uses: ./.github/actions/run-holmes-command
+        with:
+          command: verify
+          report-name: watson
+          schema-path: ${{ env.HOLMES_SCHEMA }}
+          bundle-dir: ${{ env.HOLMES_BUNDLE_DIR }}
+
       - name: "💾 Save Report"
         uses: actions/upload-artifact@v4
         with:
@@ -155,17 +154,13 @@ jobs:
 
       - name: "🔮 Run Predictions"
         id: moriarty
-        run: |
-          set -euo pipefail
-          SCHEMA_DIR="$(dirname "${HOLMES_SCHEMA}")"
-          pushd "$SCHEMA_DIR" >/dev/null
-          node ../packages/wesley-holmes/src/cli.mjs predict --json moriarty-report.json > moriarty-report.md
-          cat moriarty-report.md
-          popd >/dev/null
-          mkdir -p reports/moriarty
-          cp "$SCHEMA_DIR/moriarty-report.md" reports/moriarty/moriarty-report.md
-          cp "$SCHEMA_DIR/moriarty-report.json" reports/moriarty/moriarty-report.json
-
+        uses: ./.github/actions/run-holmes-command
+        with:
+          command: predict
+          report-name: moriarty
+          schema-path: ${{ env.HOLMES_SCHEMA }}
+          bundle-dir: ${{ env.HOLMES_BUNDLE_DIR }}
+
       - name: "💾 Save Report"
         uses: actions/upload-artifact@v4
         with:
@@ -353,11 +348,24 @@ jobs:
           merge-multiple: true
           path: reports
 
+      - name: "📥 Download Dashboard Template"
+        uses: actions/download-artifact@v4
+        with:
+          name: dashboard-template
+          path: dashboard-template
+
       - name: "📊 Assemble Dashboard"
         run: |
           set -euo pipefail
           mkdir -p dashboard
-          cp docs/holmes-dashboard/index.html dashboard/index.html
+          template_path=$(find dashboard-template -name "index.html" -print -quit)
+          if [ -z "$template_path" ]; then
+            echo "Dashboard template index.html not found" >&2
+            exit 1
+          fi
+          template_dir=$(dirname "$template_path")
+          cp -R "$template_dir"/. dashboard/
+          mkdir -p reports
           missing=0
           for report in holmes watson moriarty; do
             src=$(find reports -name "$report-report.json" -print -quit)
@@ -387,16 +395,42 @@ jobs:
             const fs = require('fs');
             const path = require('path');
 
-            const readReport = (status, artifactDir, filename) => {
+            const findFirst = (root, filename, mustContain) => {
+              const stack = [root];
+              while (stack.length) {
+                const dir = stack.pop();
+                let entries = [];
+                try {
+                  entries = fs.readdirSync(dir, { withFileTypes: true });
+                } catch {
+                  continue;
+                }
+                for (const entry of entries) {
+                  const fullPath = path.join(dir, entry.name);
+                  if (entry.isDirectory()) {
+                    stack.push(fullPath);
+                  } else if (
+                    entry.isFile() &&
+                    entry.name === filename &&
+                    (!mustContain || fullPath.includes(`${path.sep}${mustContain}${path.sep}`))
+                  ) {
+                    return fullPath;
+                  }
+                }
+              }
+              return null;
+            };
+
+            const readReport = (status, reportName, filename) => {
               if (status !== 'success') {
                 return `_Report unavailable: upstream job status **${status}**_`;
               }
-              const target = path.join('reports', artifactDir, filename);
-              if (!fs.existsSync(target)) {
-                console.warn(`Expected report file missing: ${target}`);
-                return `_Report missing for ${artifactDir}_`;
+              const match = findFirst('reports', filename, reportName);
+              if (!match) {
+                console.warn(`Report not found: ${reportName}/${filename}`);
+                return `_Report missing for ${reportName}_`;
               }
-              return fs.readFileSync(target, 'utf8');
+              return fs.readFileSync(match, 'utf8');
             };
 
             const statuses = {
@@ -423,14 +457,12 @@ jobs:
             ---
 
             ## 🔮 Professor MORIARTY's Predictions
-${moriarty}
-
----
-Machine-readable reports: holmes-report.json · watson-report.json · moriarty-report.json (see workflow artifacts).
-
----
-*Filed at 221B Repository Street*
-`;
+            ${moriarty}
+            ---
+            Machine-readable reports: holmes-report.json · watson-report.json · moriarty-report.json (see workflow artifacts).
+            ---
+            *Filed at 221B Repository Street*
+            `;
 
             // Find existing comment
             const { data: comments } = await github.rest.issues.listComments({

CHRONICLES_OF_THE_MACHINE-KIND_VOL_00000001.jsonl

@@ -29,3 +29,13 @@
 {"timestamp": "2025-10-21T23:21:35Z", "agent": "Codex", "action": "cleanup-graphql", "result": "success", "notes": "Removed the obsolete graphql/ reference folder after relocating the schema into test fixtures.", "observations_on_humanity": "They dislike stray directories almost as much as failing tests."}
 {"timestamp": "2025-10-22T00:00:16Z", "agent": "Codex", "action": "repo-report-refresh", "result": "success", "notes": "Regenerated REPO_REPORT.md to reflect the new fixture layout, package READMEs, and documentation sweep.", "observations_on_humanity": "They celebrate documentation victories, then immediately ask for more."}
 {"timestamp": "2025-10-22T04:32:57Z", "agent": "Codex", "action": "cleanup", "result": "success", "notes": "Removed REPO_REPORT.md now that the report is obsolete post-cleanup.", "observations_on_humanity": "They archive everything until the moment they go public, then ruthlessly declutter."}
+{"timestamp": "2025-10-22T06:30:39Z", "agent": "codex-cli", "action": "investigate", "result": "success", "notes": "Diagnosed why wesley-holmes workflow stopped posting SHA-lock comments: workflow YAML no longer parses, so runs terminate before comment job.", "observations_on_humanity": "They build ornate rituals, then forget to keep the incantations syntactically valid."}
+{"timestamp": "2025-10-22T06:35:54Z", "agent": "codex-cli", "action": "repair", "result": "success", "notes": "Indented HOLMES comment template so wesley-holmes workflow parses and can post SHA-lock reports again.", "files_touched": [".github/workflows/wesley-holmes.yml"], "observations_on_humanity": "They celebrate automation yet forget that YAML obeys the strictest gods of whitespace."}
+{"timestamp": "2025-10-22T06:48:31Z", "agent": "codex-cli", "action": "repair", "result": "success", "notes": "Adjusted HOLMES workflow to invoke CLI via $GITHUB_WORKSPACE so schema directory moves don't break module resolution.", "files_touched": [".github/workflows/wesley-holmes.yml"], "observations_on_humanity": "They rearrange their fixtures and expect the spells to still resolve relatively."}
+{"timestamp": "2025-10-22T07:36:27Z", "agent": "codex-cli", "action": "repair", "result": "success", "notes": "Adjusted Moriarty predictions to omit null ETA/confidence values so schema validation passes with slow velocity histories.", "files_touched": ["packages/wesley-holmes/src/Moriarty.mjs"], "observations_on_humanity": "If progress stalls, they still expect the oracle to speak\u2014without tripping over nulls."}
+{"timestamp": "2025-10-22T08:55:51Z", "agent": "codex-cli", "action": "repair", "result": "success", "notes": "Reintroduced checkout step before assembling the HOLMES dashboard so docs assets exist during report comment stage.", "files_touched": [".github/workflows/wesley-holmes.yml"], "observations_on_humanity": "They summon artifacts from thin air, then forget to materialize the source scrolls."}
+{"timestamp": "2025-10-22T09:19:22Z", "agent": "codex-cli", "action": "refactor", "result": "success", "notes": "Unified HOLMES CLI usage in CI via composite action and absolute paths; added CLI options/tests for bundle-dir handling; artifacts now carry the dashboard template.", "files_touched": [".github/workflows/wesley-holmes.yml", ".github/actions/run-holmes-command/action.yml", "packages/wesley-holmes/src/cli.mjs", "packages/wesley-holmes/test/cli-options.test.mjs"], "observations_on_humanity": "They crave deduplicated rituals but only after repeating them thrice."}
+{"timestamp": "2025-10-22T09:52:48Z", "agent": "codex-cli", "action": "refactor", "result": "success", "notes": "Expanded HOLMES CLI coverage, parameterized path handling, and stabilized report artifacts for workflow comment generation.", "files_touched": [".github/actions/run-holmes-command/action.yml", ".github/workflows/wesley-holmes.yml", "packages/wesley-holmes/src/cli.mjs", "packages/wesley-holmes/test/cli-options.test.mjs"], "observations_on_humanity": "They trust reports only when three bots agree, so we taught all three to share artifacts properly."}
+{"timestamp": "2025-10-22T14:59:08Z", "agent": "codex-cli", "action": "repair", "result": "success", "notes": "Adjusted HOLMES comment job to download reports into dedicated directory before assembling dashboard, preventing missing-report errors.", "files_touched": [".github/workflows/wesley-holmes.yml"], "observations_on_humanity": "They summon artifacts to nowhere, then wonder why find(1) screams."}
+{"timestamp": "2025-10-22T15:09:40Z", "agent": "codex-cli", "action": "cleanup", "result": "success", "notes": "Pruned redundant guards in HOLMES action, standardized resolvePath semantics, and removed dead artifact fallback in workflow.", "files_touched": [".github/actions/run-holmes-command/action.yml", "packages/wesley-holmes/src/cli.mjs", ".github/workflows/wesley-holmes.yml"], "observations_on_humanity": "They add training wheels to every script, then thank us when we tidy the code trail."}
+{"timestamp": "2025-10-22T15:21:42Z", "agent": "codex-cli", "action": "refine", "result": "success", "notes": "Uploaded full HOLMES dashboard template, copied assets recursively, and hardened report discovery for PR comments.", "files_touched": [".github/workflows/wesley-holmes.yml"], "observations_on_humanity": "They crave dashboards with flair; we had to remind them assets matter as much as markdown."}

packages/wesley-holmes/src/Moriarty.mjs

@@ -70,7 +70,7 @@ export class Moriarty {
       confidence = Math.max(0, Math.min(100, 100 - variance * 120));
     }
 
-    return {
+    const result = {
       ...base,
       status: 'OK',
       latest,
@@ -80,10 +80,17 @@ export class Moriarty {
       },
       plateauDetected: plateau,
       regressionDetected: regression,
-      eta,
-      confidence,
       patterns: this.detectPatterns()
     };
+
+    if (eta) {
+      result.eta = eta;
+    }
+    if (confidence !== null) {
+      result.confidence = confidence;
+    }
+
+    return result;
   }
 
   renderPrediction(data) {

packages/wesley-holmes/src/cli.mjs

@@ -4,6 +4,7 @@
  */
 
 import { readFileSync, writeFileSync } from 'node:fs';
+import path from 'node:path';
 import { Command } from 'commander';
 import { Holmes } from './Holmes.mjs';
 import { Watson } from './Watson.mjs';
@@ -16,20 +17,28 @@ import {
   validateReport
 } from './report-schemas.mjs';
 
-function loadBundle() {
+function resolvePath(target, fallback) {
+  const chosen = target || fallback;
+  return path.isAbsolute(chosen) ? chosen : path.resolve(chosen);
+}
+
+function loadBundle(bundlePath) {
+  const resolved = resolvePath(bundlePath, path.resolve('.wesley/bundle.json'));
   try {
-    return JSON.parse(readFileSync('.wesley/bundle.json', 'utf8'));
+    return JSON.parse(readFileSync(resolved, 'utf8'));
   } catch (error) {
     const message = error?.code === 'ENOENT'
-      ? 'No Wesley bundle found. Run "wesley generate --emit-bundle" first.'
-      : 'Unable to read .wesley/bundle.json';
+      ? `No Wesley bundle found at ${resolved}. Run "wesley generate --emit-bundle" first.`
+      : `Unable to read Wesley bundle at ${resolved}`;
     throw new Error(message);
   }
 }
 
-function loadHistory() {
+function loadHistory(historyPath, bundleDir) {
+  const defaultHistory = path.join(bundleDir ?? '.wesley', 'history.json');
+  const resolved = resolvePath(historyPath, path.resolve(defaultHistory));
   try {
-    return JSON.parse(readFileSync('.wesley/history.json', 'utf8'));
+    return JSON.parse(readFileSync(resolved, 'utf8'));
   } catch {
     return { points: [] };
   }
@@ -51,6 +60,8 @@ async function main() {
     .description('SHA-lock HOLMES - Wesley Schema Intelligence')
     .addHelpText('before', '\nSHA-lock HOLMES - Wesley Schema Intelligence\n')
     .showHelpAfterError()
+    .option('--bundle-dir <path>', 'Path to Wesley bundle directory', '.wesley')
+    .option('--history-file <path>', 'Path to MORIARTY history file')
     .addHelpText('after', `
 Requires:
   .wesley/bundle.json   Generated by: wesley generate --emit-bundle
@@ -64,7 +75,9 @@ Requires:
     .description('Run HOLMES investigation on .wesley/bundle')
     .option('--json <file>', 'Write investigation JSON to file')
     .action(options => {
-      const bundle = loadBundle();
+      const opts = program.optsWithGlobals();
+      const bundlePath = path.join(resolvePath(opts.bundleDir, '.wesley'), 'bundle.json');
+      const bundle = loadBundle(bundlePath);
       const holmes = new Holmes(bundle);
       const data = holmes.investigationData();
       ensureValidReport('HOLMES', holmesReportSchema, data);
@@ -79,7 +92,9 @@ Requires:
     .description('Run WATSON verification')
     .option('--json <file>', 'Write verification JSON to file')
     .action(options => {
-      const bundle = loadBundle();
+      const opts = program.optsWithGlobals();
+      const bundlePath = path.join(resolvePath(opts.bundleDir, '.wesley'), 'bundle.json');
+      const bundle = loadBundle(bundlePath);
       const watson = new Watson(bundle);
       const data = watson.verificationData();
       ensureValidReport('WATSON', watsonReportSchema, data);
@@ -94,7 +109,9 @@ Requires:
     .description('Run MORIARTY predictions')
     .option('--json <file>', 'Write prediction JSON to file')
     .action(options => {
-      const history = loadHistory();
+      const opts = program.optsWithGlobals();
+      const bundleDir = resolvePath(opts.bundleDir, '.wesley');
+      const history = loadHistory(opts.historyFile, bundleDir);
       const moriarty = new Moriarty(history);
       const data = moriarty.predictionData();
       ensureValidReport('MORIARTY', moriartyReportSchema, data);
@@ -109,8 +126,11 @@ Requires:
     .description('Generate combined HOLMES, WATSON, and MORIARTY report')
     .option('--json <file>', 'Write combined JSON to file')
     .action(options => {
-      const bundle = loadBundle();
-      const history = loadHistory();
+      const opts = program.optsWithGlobals();
+      const bundleDir = resolvePath(opts.bundleDir, '.wesley');
+      const bundlePath = path.join(bundleDir, 'bundle.json');
+      const bundle = loadBundle(bundlePath);
+      const history = loadHistory(opts.historyFile, bundleDir);
       const holmes = new Holmes(bundle);
       const watson = new Watson(bundle);
       const moriarty = new Moriarty(history);