fix: CodeGit looked like an empty black box - hardcoded panel height + cache

Reported as "why can't i see anything from codegit its just a black box".

NOT a codegit bug. Verified first, exhaustively, through the authenticated API:
  overview  200    940 bytes
  log       200  79596 bytes   (full commit history)
  transfer  200   1460 bytes
  config    200   1174 bytes
no JS errors in the console; every DOM helper codegit calls exists.

ROOT CAUSE 1 - a generic CSS rule hardcodes a height
  theme/modules/common/_panel.scss -> theme/main.min.css:
    panel { ... height: 500px; ... }
  That forces EVERY modal panel to a fixed 500px box. Measured live:
    #dialog            404px  (clamped by max-height:70vh + overflow-y:auto)
    #codegit panel     500px, while its content is only 119px
    toolbar ("Branch") top 620 vs dialog bottom 490 -> OUTSIDE the modal
  So ~380px of the dialog was empty dead space and the Branch line rendered below the
  modal, invisible. Fixed to height:auto with max-height:58vh (long content still scrolls):
    before: panel 500 -> toolbar top 620, dialog bottom 490 (outside)
    after:  panel 136 -> toolbar top 256, dialog bottom 279 (inside)
  _panel.scss updated too so the source does not contradict the shipped CSS.

ROOT CAUSE 2 - the fix was invisible because of the browser cache
  Atheos serves theme/main.min.css and the generated bundles from stable URLs with no cache
  headers, so browsers legitimately reuse their cached copy - which is why the first attempt
  appeared to do nothing. nginx now sends Cache-Control: no-cache, must-revalidate for
  *.css/*.js: caching still works (cheap 304s) but changes are always picked up.

Adds
  scripts/fix-panel-layout.sh   idempotent re-apply for both fixes (lost on update-atheos)
  docs/known-issues.md §4, §5   both findings, with the measurements

Tests (44 passed, 1 failed - the failure is branch protection, a genuine open item)
  + panel must not be fixed at 500px
  + theme CSS must send Cache-Control: no-cache

docs/known-issues.md

@@ -224,7 +224,79 @@ Worth doing if the dialog starts 500-ing again after editing a macro in the UI.
 
 ---
 
-## 4. Checking for plugin problems in future
+## 4. 🟠 The CodeGit panel looked like an empty black box
+
+**Symptom:** the CodeGit dialog appeared as a mostly-empty black rectangle. Nothing was *broken* —
+it was unreadable, which reads as "broken".
+
+**This was NOT a codegit bug.** Verified exhaustively first:
+
+```
+all four panels return real content through the authenticated API:
+  overview   200    940 bytes
+  log        200  79596 bytes   (full commit history)
+  transfer   200   1460 bytes
+  config     200   1174 bytes
+no JS errors in the browser console; all DOM helpers (replaceClass etc.) exist
+```
+
+**Root cause — the generic `panel` rule hardcodes a height.** `theme/modules/common/_panel.scss`
+(after minification, in `theme/main.min.css`):
+
+```css
+panel { padding: 5px; width: calc(100% - 200px); overflow: auto; overflow-y: scroll;
+        height: 500px; position: relative; border-left: var(--borderLight); }
+```
+
+Measured live, that produces:
+
+| Element | Height | Problem |
+|---|---|---|
+| `#dialog` | 404px | clamped by `max-height: 70vh` + `overflow-y: auto` |
+| `#codegit panel` | 500px | **forced**, while its content is 119px |
+| `toolbar` ("Branch: …") | top **620** vs dialog bottom **490** | **pushed OUTSIDE the modal** |
+
+So ~380px of the dialog was **empty dead space**, and anything after the panel — including the
+Branch line — rendered *below* the modal, invisible. A generic `panel { height: 500px }` is exactly
+the kind of rule that looks like a void.
+
+**Fix applied:**
+
+```css
+panel { ... height: auto; max-height: 58vh; overflow-y: auto; ... }
+```
+
+Content-sized, capped so long content (the 79KB log) still scrolls. Verified live:
+
+```
+before: panel 500px  → toolbar top 620, dialog bottom 490   (outside)
+after:  panel 136px  → toolbar top 256, dialog bottom 279   (inside)
+```
+
+`theme/modules/common/_panel.scss` is updated too, so the source does not contradict the shipped CSS
+(there is no Sass compiler on the guest, so `main.min.css` is edited directly).
+
+---
+
+## 5. 🟠 CSS/JS changes were invisible behind the browser cache
+
+**Symptom:** a fix to the theme did not appear until a hard refresh — so the panel fix above looked
+like it had not worked at all.
+
+**Root cause:** Atheos serves `theme/main.min.css` and the generated `public/*.min.js|css` bundles
+from **stable URLs with no cache headers**, so nginx adds only `Last-Modified`/`ETag` and browsers
+legitimately reuse their cached copy.
+
+**Fix:** nginx now sends `Cache-Control: no-cache, must-revalidate` for `*.css`/`*.js`. Note this does
+**not** disable caching — it forces **revalidation**, so normal loads still get a cheap 304 while any
+change is guaranteed to be picked up on the next load.
+
+**If you ever see a stale UI again:** force a reload (Ctrl/Cmd-Shift-R). That is the first thing to try
+before assuming a fix failed.
+
+---
+
+## 6. Checking for plugin problems in future
 
 The plugin's JS is bundled into `public/plugins.min.js` (built by `classes/sourcemanager.php`), and
 its rightbar button is rendered by `components/sidebars/sb-right.php` from `plugin.json`. Both were
@@ -258,17 +330,17 @@ verify them before trusting it.
 
 ---
 
-## 5. Follow-ups not done (recorded so they are not forgotten)
+## 7. Follow-ups not done (recorded so they are not forgotten)
 
 These came out of review. They are **operator decisions**, not agent ones — several change what the
 editor can do.
 
-### 5.1 Remove the Terminal plugin — ✅ DONE
+### 7.1 Remove the Terminal plugin — ✅ DONE
 
 Removed through the market's own code path once §1 was fixed (see §2). A browser shell was the largest
 attack surface in the container and macros already cover command execution.
 
-### 5.2 ❌ `disable_functions` cannot be "on by default" here — measured
+### 7.2 ❌ `disable_functions` cannot be "on by default" here — measured
 
 Review asked for `php.ini` to disable `exec`, `shell_exec`, `passthru`, `system` by default.
 **This would break the editor's core function.** Evidence:
@@ -285,18 +357,18 @@ turns the editor into a text editor that cannot commit. So it stays **a delibera
 you would also lose macros and git integration, which is why S-7 already says *"test, do not
 blind-apply"*.
 
-### 5.3 Rotate the terminal password automatically
+### 7.3 Rotate the terminal password automatically
 
 If the plugin is kept, `provision.sh` should generate a random password rather than leaving the
 upstream default. Not implemented: it would hardcode a secret into a repo file, which is the same
 class of problem this file already documents.
 
-### 5.4 Deploy key could be read-only
+### 7.4 Deploy key could be read-only
 
 Review suggested making the deploy key read-only if writes are unnecessary. **They are necessary** —
 that is the whole point of the writer-branch workflow (macro 2 pushes). Not applicable.
 
-### 5.5 The real upstream fix for §3
+### 7.5 The real upstream fix for §3
 
 `class.macro.php::save()` should write `[]` instead of `"N/A"` for folder macros. See §3 — the fix is
 currently applied to the data, so it survives updates, at the cost of being reversible from the UI.

files/atheos.conf

@@ -7,13 +7,12 @@ server {
     root /var/www/atheos;
     index index.php index.html;
 
+    # --- logging ---------------------------------------------------------
     access_log /var/log/nginx/atheos.access.log;
     error_log  /var/log/nginx/atheos.error.log;
 
-    # --- PHP -----------------------------------------------------------------
+    # --- PHP: the socket path here MUST byte-match the pool's `listen =`
-    # The socket path here MUST byte-match the pool's `listen =` in
+    #     in /etc/php83/php-fpm.d/www.conf  (interface I-1 -> else bare 502)
-    #   /etc/php83/php-fpm.d/www.conf
-    # (interface I-1 — a mismatch yields a bare 502 with no other diagnostic).
     location ~ \.php$ {
         try_files $uri =404;
         fastcgi_split_path_info ^(.+\.php)(/.+)$;
@@ -27,7 +26,8 @@ server {
         try_files $uri $uri/ =404;
     }
 
-    # --- hardening -----------------------------------------------------------
+    # --- hardening (free, no downside) -----------------------------------
+    # never serve the VCS directory, the app's private data, or dotfiles
     location ~ /\.git       { deny all; }
     location ~ /\.ssh       { deny all; }
     location ~ /\.           { deny all; }
@@ -40,4 +40,13 @@ server {
     add_header Referrer-Policy "strict-origin-when-cross-origin" always;
 
     client_max_body_size 64m;
+
+    # Atheos serves theme/main.min.css and the generated *.min.js/css bundles from STABLE URLs
+    # with no cache headers. Without this, a CSS/JS change stays invisible behind a cached copy
+    # until the user hard-refreshes. "no-cache" permits caching but forces revalidation, so a
+    # 304 keeps normal loads fast while guaranteeing updates are picked up on the next load.
+    location ~* \.(css|js)$ {
+        add_header Cache-Control "no-cache, must-revalidate";
+        try_files $uri =404;
+    }
 }

scripts/build-and-test.sh

@@ -106,11 +106,31 @@ for d in mysqld mariadbd postgres redis-server; do
   if command -v "$d" >/dev/null 2>&1; then bad "$d present - unexpected"; else ok "$d absent (correct)"; fi
 done
 
+echo
+echo "=============================================================="
+echo "REGRESSION: panel has no hardcoded height (empty-modal bug)"
+echo "=============================================================="
+# panel { height:500px } forced every modal panel to a fixed box: short content left a large
+# empty black region and anything after the panel (codegit's Branch toolbar) was pushed outside
+# the modal. docs/known-issues.md §4. Fails loudly if lost to an update.
+PNL=$(grep -oE '(^|[;}])panel\{[^}]*\}' /var/www/atheos/theme/main.min.css 2>/dev/null | head -1)
+if [ -z "$PNL" ]; then
+  bad "could not read the panel rule from theme/main.min.css"
+elif echo "$PNL" | grep -q 'height:500px'; then
+  bad "panel is fixed at 500px - re-run scripts/fix-panel-layout.sh"
+else
+  ok "panel is content-sized ($(echo "$PNL" | grep -oE 'height:[^;]*' | head -1))"
+fi
+# and the CSS/JS cache header must be present, or fixes stay invisible
+if wget -qO /dev/null --server-response --header='Host: 127.0.0.1' http://127.0.0.1/theme/main.min.css 2>&1 | grep -qi 'Cache-Control.*no-cache'; then
+  ok "theme CSS sends Cache-Control: no-cache (changes are picked up)"
+else
+  bad "theme CSS has no Cache-Control - a CSS fix can stay hidden behind the browser cache"
+fi
 echo
 echo "=============================================================="
 echo "REGRESSION: rDelete works (GLOB_BRACE is glibc-only; musl lacks it)"
 echo "=============================================================="
-# traits/helpers.php::rDelete() used GLOB_BRACE, which is undefined under musl -> PHP 8 fatal.
 # That broke deleting ANY file/folder in the editor AND removing a market plugin (the UI
 # would spin forever because the fatal killed the response before Common::send()).
 # docs/known-issues.md §1. This test fails loudly if the patch is lost (e.g. by an update).

scripts/fix-panel-layout.sh

@@ -0,0 +1,76 @@
+#!/bin/sh
+# Re-apply the UI/layout fixes to a rebuilt or updated Atheos tree.
+#
+# Why this exists: Atheos has no releases and `scripts/update-atheos.sh` replaces the whole
+# application directory, so any local patch is lost on update. These are the two that were
+# needed to make the editor usable. Both are IDEMPOTENT - run it as often as you like.
+#
+#   1. panel { height: 500px }      ->  height:auto; max-height:58vh
+#      Every modal panel was forced to a fixed 500px box, so dialogs with short content showed
+#      a large empty black region and anything after the panel (codegit's "Branch:" toolbar)
+#      was pushed OUTSIDE the modal. See docs/known-issues.md §4.
+#
+#   2. nginx: Cache-Control: no-cache for *.css/*.js
+#      Theme/bundle changes were invisible behind the browser cache. §5.
+#
+# Usage:  sh scripts/fix-panel-layout.sh          (run ON the guest, as root)
+set -e
+
+ATH=/var/www/atheos
+CSS=$ATH/theme/main.min.css
+SCSS=$ATH/theme/modules/common/_panel.scss
+NGX=/etc/nginx/http.d/atheos.conf
+
+echo "=== 1. panel layout ==="
+OLD='height:500px;position:relative;border-left:var(--borderLight)'
+NEW='height:auto;max-height:58vh;position:relative;border-left:var(--borderLight)'
+if [ ! -f "$CSS" ]; then
+  echo "  !! $CSS not found - is Atheos installed?"
+elif grep -qF "$NEW" "$CSS"; then
+  echo "  already applied"
+elif grep -qF "$OLD" "$CSS"; then
+  [ -f "$CSS.orig" ] || cp -a "$CSS" "$CSS.orig"
+  php83 -r '$f=$argv[1];$o=$argv[2];$n=$argv[3];$s=file_get_contents($f);
+            if(strpos($s,$o)===false){exit(1);} file_put_contents($f,str_replace($o,$n,$s));' "$CSS" "$OLD" "$NEW"
+  echo "  applied to main.min.css"
+else
+  echo "  !! expected panel rule not found - inspect manually"
+  echo "     (upstream may have changed it; diff against $CSS.orig)"
+fi
+
+# keep the SCSS source consistent so the shipped CSS is not contradicted by the source
+if [ -f "$SCSS" ] && grep -q 'height: 500px;' "$SCSS"; then
+  [ -f "$SCSS.orig" ] || cp -a "$SCSS" "$SCSS.orig"
+  php83 -r '$f=$argv[1];$s=file_get_contents($f);
+            $s=str_replace("height: 500px;","height: auto;\n\tmax-height: 58vh;",$s);
+            file_put_contents($f,$s);' "$SCSS"
+  echo "  synchronised _panel.scss"
+fi
+
+echo "=== 2. nginx cache headers ==="
+if [ ! -f "$NGX" ]; then
+  echo "  !! $NGX not found"
+elif grep -q 'must-revalidate' "$NGX"; then
+  echo "  already applied"
+else
+  [ -f "$NGX.orig" ] || cp -a "$NGX" "$NGX.orig"
+  cat > /tmp/.cacheblock <<'EOF'
+
+    # Atheos serves theme/main.min.css and the generated *.min.js/css bundles from STABLE URLs
+    # with no cache headers, so a CSS/JS fix stays invisible behind the browser cache until a
+    # hard refresh. "no-cache" permits caching but forces revalidation: normal loads still get a
+    # cheap 304, and a change is guaranteed to be picked up on the next load.
+    location ~* \.(css|js)$ {
+        add_header Cache-Control "no-cache, must-revalidate";
+        try_files $uri =404;
+    }
+EOF
+  php83 -r '$f=$argv[1];$b=$argv[2];$s=file_get_contents($f);
+            $p=strrpos($s,"}"); if($p===false){exit(1);}
+            file_put_contents($f,substr($s,0,$p).file_get_contents($b).substr($s,$p));' "$NGX" /tmp/.cacheblock
+  rm -f /tmp/.cacheblock
+  nginx -t >/dev/null 2>&1 && rc-service nginx reload >/dev/null 2>&1 && echo "  applied + nginx reloaded" \
+    || echo "  !! nginx -t failed - restore $NGX.orig"
+fi
+
+echo "=== done ==="