14 fix the deployment error

.github/workflows/theseus-engine.yml

@@ -33,6 +33,13 @@ jobs:
       - name: Run theseus multi-repo analysis (delta load)
         run: poetry run python scripts/analyse_repository.py
 
+      - name: Update living fossils (survivor check)
+        run: |
+          # Re-blame HEAD for every repo and update the survivor fossil only if
+          # the file:line:commit has actually changed since the last run.
+          # Genesis (historical fossil) is left completely untouched.
+          poetry run python scripts/add_fossils.py --update-survivor
+
       - name: Commit and push data updates
         run: |
           git config --local user.email "action@github.com"

app.js

@@ -30,12 +30,13 @@ class TheseusVisualizer {
 
     async init() {
         try {
-            const response = await fetch('data/manifest.json');
+            const response = await fetch('theseus.config.json');
             if (!response.ok) {
                 throw new Error(`HTTP ${response.status}`);
             }
             let data = await response.json();
-            this.manifest = Array.isArray(data) ? data : [data];
+            // Fallback for backward compatibility, but normally expected to be under 'repositories'
+            this.manifest = data.repositories || (Array.isArray(data) ? data : [data]);
 
             this.renderSelectors();
             this.setupModeToggle();
@@ -406,7 +407,7 @@ class TheseusVisualizer {
                 const idx = bisect(this.points, date, 1);
                 const d0 = this.points[idx - 1];
                 const d1 = this.points[idx];
-                
+
                 // Handle single-point or edge cases
                 if (!d0 && !d1) return;
                 let d;
@@ -447,17 +448,17 @@ class TheseusVisualizer {
         let refactorHTML = '';
         if (originalVal === 0) {
             refactorHTML = `
-                <div style="background: rgba(248, 113, 113, 0.15); border: 1px solid rgba(248, 113, 113, 0.4); 
-                            padding: 1rem; border-radius: 1rem; margin-bottom: 1.25rem; color: #f87171; 
+                <div style="background: rgba(248, 113, 113, 0.15); border: 1px solid rgba(248, 113, 113, 0.4);
+                            padding: 1rem; border-radius: 1rem; margin-bottom: 1.25rem; color: #f87171;
                             font-size: 0.85rem; line-height: 1.5;">
                     <strong style="display: block; margin-bottom: 0.35rem; text-transform: uppercase; letter-spacing: 0.05em;">Ship of Theseus: The Great Rebirth</strong>
                     The original source code is now entirely gone.<br/><strong>Is this still the same codebase?</strong>
                 </div>
             `;
         } else if (isRefactor) {
             refactorHTML = `
-                <div style="background: rgba(240, 163, 59, 0.15); border: 1px solid rgba(240, 163, 59, 0.4); 
-                            padding: 0.75rem; border-radius: 0.75rem; margin-bottom: 1rem; color: #f0a33b; 
+                <div style="background: rgba(240, 163, 59, 0.15); border: 1px solid rgba(240, 163, 59, 0.4);
+                            padding: 0.75rem; border-radius: 0.75rem; margin-bottom: 1rem; color: #f0a33b;
                             font-size: 0.85rem; line-height: 1.4;">
                     <strong style="display: block; margin-bottom: 0.25rem;">Ship of Theseus: Major Refactor</strong>
                     A significant part of the original source was refactored here.<br/>How much can you change before the identity shifts?
@@ -653,24 +654,47 @@ class TheseusVisualizer {
         const repoPath = repoInfo ? repoInfo.repo : null;
 
         const buildLink = (fossil) => {
-            if (!fossil.file) return '--';
-            const display = `${fossil.file}:${fossil.line}`;
-            if (!repoPath || !fossil.commit) return display;
-            const url = `https://github.com/${repoPath}/blob/${fossil.commit}/${fossil.file}#L${fossil.line}`;
-            return `<a href="${url}" target="_blank" rel="noopener noreferrer" style="color: inherit; text-decoration: underline; text-decoration-color: rgba(255,255,255,0.2); transition: color 0.3s ease;" onmouseover="this.style.color='var(--accent-cyan)'" onmouseout="this.style.color='inherit'">${display}</a>`;
+            const display = fossil.file ? `${fossil.file}:${fossil.line}` : '--';
+
+            // No file or no repo → plain text node, nothing to link
+            if (!fossil.file || !repoPath) return document.createTextNode(display);
+
+            const linkCommit = fossil.view_commit || fossil.commit;
+            if (!linkCommit) return document.createTextNode(display);
+
+            // URL-encode the file path (preserve /, encode special chars per segment)
+            // and the commit ref (branch names can contain slashes so encode fully)
+            const safeFile = fossil.file.split('/').map(encodeURIComponent).join('/');
+            const safeCommit = encodeURIComponent(linkCommit);
+            const safeLine = parseInt(fossil.line, 10) || 0;
+            const url = `https://github.com/${repoPath}/blob/${safeCommit}/${safeFile}#L${safeLine}`;
+
+            const a = document.createElement('a');
+            a.href = url;
+            a.target = '_blank';
+            a.rel = 'noopener noreferrer';
+            a.textContent = display;
+            a.style.color = 'inherit';
+            a.style.textDecoration = 'underline';
+            a.style.textDecorationColor = 'rgba(255,255,255,0.2)';
+            a.style.transition = 'color 0.3s ease';
+            a.addEventListener('mouseover', () => { a.style.color = 'var(--accent-cyan)'; });
+            a.addEventListener('mouseout', () => { a.style.color = 'inherit'; });
+            return a;
         };
 
-        // Genesis (The Origin)
+        // Genesis (Historical Fossil) — show the pinned blame commit hash (frozen in history)
         document.getElementById('genesis-year').textContent = genesis.year || '----';
-        document.getElementById('genesis-file').innerHTML = buildLink(genesis);
+        document.getElementById('genesis-file').replaceChildren(buildLink(genesis));
         document.getElementById('genesis-content').textContent = genesis.content ? genesis.content.trim() : 'No fossil data';
         document.getElementById('genesis-commit').textContent = genesis.commit || '';
 
-        // Survivor (The Current)
+        // Survivor (Living Fossil) — show branch name (e.g. "main"), not old blame hash
         document.getElementById('survivor-year').textContent = survivor.year || '----';
-        document.getElementById('survivor-file').innerHTML = buildLink(survivor);
+        document.getElementById('survivor-file').replaceChildren(buildLink(survivor));
         document.getElementById('survivor-content').textContent = survivor.content ? survivor.content.trim() : 'No fossil data';
-        document.getElementById('survivor-commit').textContent = survivor.commit || '';
+        document.getElementById('survivor-commit').textContent = survivor.view_commit || survivor.commit || '';
+
     }
 
     createSVGElement(tag, attrs = {}) {
@@ -680,7 +704,20 @@ class TheseusVisualizer {
     }
 
     showLoading(show) {
-        this.loadingState.classList.toggle('hidden', !show);
+        if (show) {
+            this.loadingState.classList.remove('hidden');
+            // Also hide the chart container while skeleton shows
+            const chartContainer = document.getElementById('chart-container');
+            if (chartContainer) chartContainer.style.opacity = '0';
+        } else {
+            this.loadingState.classList.add('hidden');
+            // Fade the chart back in smoothly
+            const chartContainer = document.getElementById('chart-container');
+            if (chartContainer) {
+                chartContainer.style.transition = 'opacity 0.35s ease';
+                chartContainer.style.opacity = '1';
+            }
+        }
     }
 
     showError(msg) {

data/claude-code_data.json

@@ -1 +1 @@
-{"snapshots":[{"snapshot_date":"2025-02","composition":{"2025":315}},{"snapshot_date":"2025-03","composition":{"2025":368}},{"snapshot_date":"2025-04","composition":{"2025":455}},{"snapshot_date":"2025-05","composition":{"2025":756}},{"snapshot_date":"2025-06","composition":{"2025":876}},{"snapshot_date":"2025-07","composition":{"2025":77387}},{"snapshot_date":"2025-08","composition":{"2025":77900}},{"snapshot_date":"2025-09","composition":{"2025":78823}},{"snapshot_date":"2025-10","composition":{"2025":56350}},{"snapshot_date":"2025-11","composition":{"2025":60301}},{"snapshot_date":"2025-12","composition":{"2025":86284}},{"snapshot_date":"2026-01","composition":{"2025":86626,"2026":35}},{"snapshot_date":"2026-02","composition":{"2025":86420,"2026":653}},{"snapshot_date":"2026-03","composition":{"2025":86142,"2026":1705}},{"snapshot_date":"2026-04","composition":{"2025":86142,"2026":2431}}],"fossils":{"genesis":{"timestamp":1740245022,"file":".devcontainer/Dockerfile","content":"FROM node:20","year":"2025","commit":"bd5ca70","line":1},"survivor":{"timestamp":1740245022,"file":".devcontainer/Dockerfile","content":"FROM node:20","year":"2025","commit":"bd5ca70","line":1}}}
+{"snapshots":[{"snapshot_date":"2025-02","composition":{"2025":315}},{"snapshot_date":"2025-03","composition":{"2025":368}},{"snapshot_date":"2025-04","composition":{"2025":455}},{"snapshot_date":"2025-05","composition":{"2025":756}},{"snapshot_date":"2025-06","composition":{"2025":876}},{"snapshot_date":"2025-07","composition":{"2025":77387}},{"snapshot_date":"2025-08","composition":{"2025":77900}},{"snapshot_date":"2025-09","composition":{"2025":78823}},{"snapshot_date":"2025-10","composition":{"2025":56350}},{"snapshot_date":"2025-11","composition":{"2025":60301}},{"snapshot_date":"2025-12","composition":{"2025":86284}},{"snapshot_date":"2026-01","composition":{"2025":86626,"2026":35}},{"snapshot_date":"2026-02","composition":{"2025":86420,"2026":653}},{"snapshot_date":"2026-03","composition":{"2025":86142,"2026":1705}},{"snapshot_date":"2026-04","composition":{"2025":86142,"2026":2431}}],"fossils":{"genesis":{"timestamp":1740245022,"file":".devcontainer/Dockerfile","content":"FROM node:20","year":"2025","commit":"bd5ca70","view_commit":"bd5ca708adf82c4b81857abf40fe36d9d9cc3d1c","line":1},"survivor":{"timestamp":1740245022,"file":".devcontainer/init-firewall.sh","content":"#!/bin/bash","year":"2025","commit":"bd5ca70","view_commit":"main","line":1}}}

data/langchain_data.json

@@ -1 +1 @@
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