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

@@ -0,0 +1,374 @@
+# Known Issues & Patches
+
+Upstream Atheos is an actively-moving project with **no releases**, and its plugin market ships
+plugins that are **ports from Codiad** (Atheos's predecessor). Two of those plugins use APIs that
+Atheos has since removed or changed. This file records what we hit, what we changed, and why the
+fix is done the way it is.
+
+Pinned Atheos commit: `f90cd1806dbe0e25673a77e27390e8b1a240c3f6` (build 611).
+
+---
+
+## 1. 🔴 **Deleting any file or folder was broken** — `GLOB_BRACE` does not exist on musl
+
+**Symptom:** removing the Terminal plugin from the market **cycled forever in the UI** (never
+completed, never errored). Deleting a file or folder in the editor was broken by the same cause.
+
+**Root cause — a glibc-only constant referenced on musl.** `traits/helpers.php::rDelete()`:
+
+```php
+$files = glob($target . "{*,.[!.]*,..?*}", GLOB_BRACE|GLOB_MARK);
+```
+
+`GLOB_BRACE` is a **glibc extension**. Alpine uses **musl**, where the constant is *undefined* —
+and touching an undefined constant is a **fatal error** in PHP 8 (a warning in older versions):
+
+```
+PHP Fatal error: Uncaught Error: Undefined constant "GLOB_BRACE"
+in /var/www/atheos/traits/helpers.php:138
+#0 components/market/class.market.php(178): Common::rDelete()
+#1 components/market/controller.php(46): Market->remove()
+```
+
+Because the fatal kills the request before `Common::send(200)`, the front end never receives a
+settle response — so the UI **spins indefinitely**. A hang, not an error.
+
+**Blast radius — measured, two call sites:**
+
+| Caller | What breaks |
+|---|---|
+| `components/market/class.market.php:178` | removing a plugin from the market |
+| `components/filetree/class.filetree.php:59` | **deleting any file or folder in the editor** |
+
+The second is core editor functionality, so this is **not** a plugin bug — installing the Terminal
+plugin is merely what made it visible. Verified directly: with the original code, `rDelete()` fatals
+and the target is left on disk.
+
+**Fix applied** (`patches/helpers-rDelete-GLOB_BRACE.diff`) — expand the brace pattern by hand when
+`GLOB_BRACE` is absent, keeping upstream's exact behaviour where it *is* defined:
+
+```php
+if (defined("GLOB_BRACE")) {
+    $files = glob($target . "{*,.[!.]*,..?*}", GLOB_BRACE | GLOB_MARK);
+} else {
+    $files = array_merge(
+        glob($target . "/*",        GLOB_MARK) ?: [],
+        glob($target . "/.[!.]*",   GLOB_MARK) ?: [],
+        glob($target . "/..?*",     GLOB_MARK) ?: []
+    );
+}
+```
+
+The three patterns are precisely what the brace expansion produces (`*`, dotfiles, and `.`/`..`-like
+names), so the directory listing is equivalent.
+
+**Verified** — `php83 -l` clean, then a real deletion of a tree containing nested dirs and two
+dotfiles:
+
+```
+entries before: 10
+rDelete() returned: true
+exists after: gone (OK)
+single file: rDelete=true exists=gone (OK)
+```
+
+**Upstream has NOT fixed this** — the same line is still in `main` (checked directly), so it cannot
+be resolved by updating Atheos. Re-apply this patch after any update (`scripts/update-atheos.sh`).
+
+**Consequence for the platform choice:** this is the real cost of Alpine. A glibc-based image
+(Debian/Ubuntu) would not have hit it. It is patchable in one place, so Alpine stays — but it is worth
+knowing that `GLOB_BRACE` is the kind of thing musl breaks.
+
+---
+
+## 2. 🔴 Plugin market: the **Terminal** plugin does not work as shipped
+
+**Symptom:** installed the Terminal plugin from the market; it failed / did not function.
+
+**Root cause — a removed API.** `plugins/Terminal/terminal.php` calls `Common::execute(...)`, which
+**no longer exists** in Atheos (it was renamed):
+
+```
+plugin calls : Common::execute(...)      ->  MISSING
+available    : Common::raw_execute(...)  ->  returns ["code" => int, "output" => array]
+                Common::safe_execute(...)
+```
+
+The plugin's header says it is a port of `Fluidbyte/Codiad-Terminal`, so it targets the old API. Its
+return-shape assumption is also stale (the old `execute()` returned `text`; `raw_execute()` returns
+`output` as an array).
+
+**Fix applied** (`patches/Terminal-terminal.php.patched`):
+
+```diff
+-  $output = Common::execute("pwd");
++  $output = Common::raw_execute("pwd");
+-  $_SESSION["activeDir"] = array([$_SESSION["project"]] => $output["text"]);
++  $_SESSION["activeDir"] = array([$_SESSION["project"]] => implode("\n", (array)$output["output"]));
+
+-  $output = Common::execute($cmd);
+-  return $output["text"];
++  $output = Common::raw_execute($cmd);
++  return implode("\n", (array)$output["output"]);
+```
+
+**Verified** against the real method (`php83 -l` clean; both call patterns exercised):
+
+| Call | Result |
+|---|---|
+| `raw_execute("pwd")` | `code=0`, `output=["/root",""]` |
+| `raw_execute("echo ...")` | `code=0`, returns the text |
+| after `chdir` to the repo | returns `/var/www/atheos/workspace/blog` — so the terminal opens in the blog |
+
+**Re-apply after an Atheos update** — `scripts/update-atheos.sh` replaces the application files, so
+this patch is lost on update. Re-apply it, or drop the plugin.
+
+### Two further defects in the same plugin (NOT fixed — upstream, and mostly harmless)
+
+1. **`terminal.php:95`** — `$blocked = explode(",", BLOCKED === true);` passes a **boolean** to
+   `explode()`. This evaluates to `explode(",", false)`, so the intended block-list
+   (`define("BLOCKED","ssh,telnet")`) **never actually blocks anything**. The plugin's own guard is
+   dead code. Cosmetic in effect (the command would just fail on its own), but worth knowing rather
+   than trusting.
+2. **`terminal.php:124`** — `if (strtolower($command === "exit"))` passes a boolean to
+   `strtolower()`. Should be `strtolower($command) === "exit"`. Result: typing `exit` does not clear
+   `term_auth`; the session stays authenticated until the browser session ends.
+
+Left as-is: they are upstream bugs, and fixing them changes the plugin's behaviour beyond the
+minimum needed to make it run. Recorded here so nobody "fixes" them by accident or trusts the
+block-list.
+
+### ⚠️ Security note
+
+This plugin gives a **browser terminal that executes shell commands as the php-fpm user**
+(`atheos`). Two things matter:
+
+1. **The plugin ships with a well-known, hardcoded gate constant.** Upstream is literally
+   `define("PASSWORD", "<the default value in the plugin source>");`. Anyone who can reach the page
+   can read the source on GitHub and unlock it. **We have rotated it to a random value** — retrieve
+   it from the `PASSWORD` define in `plugins/Terminal/terminal.php` on the guest. It is deliberately
+   **not recorded in this repo** (see below).
+2. **It is a shell, so treat it as a privilege decision, not a convenience one.** Installing it
+   means the editor can run arbitrary commands as `atheos` — the same user that owns the deploy key.
+
+Because of (1) and (2), the in-app password is treated as a **secret**:
+
+- it is **not** written into this repo, the README, or the RUNBOOK
+- to read it: `ssh root@192.168.178.57 'grep PASSWORD /var/www/atheos/plugins/Terminal/terminal.php'`
+- it changes per install; `scripts/provision.sh` does not set one, so a rebuild returns to the
+  upstream default — **rotate it again after a rebuild**
+
+**Outcome: the plugin has been REMOVED.** Once the `GLOB_BRACE` fault (§1) was fixed, removal through
+the market succeeded — and that is the right end state: a browser shell is the single largest attack
+surface in the container, and **Atheos macros already provide command execution**, so it added little
+you did not already have. Removal was done by invoking the market's own `remove()` path, so the plugin
+list, the `addons` cache and the generated bundle all stayed consistent:
+
+```
+{"text":"Plugin successfully removed.","status":200}
+plugins/ -> (only README.md remains)
+addons cache references to Terminal: 0
+```
+
+The notes above are kept because they document what the plugin *is* and how it failed — and because
+the same stale-API pattern will recur with any other Codiad-era plugin. To reinstall, use the
+market: it will re-introduce the `Common::execute` fault, so `patches/Terminal-terminal.php.patched`
+was the fix — **it has been deleted along with the plugin**. If you ever reinstall, re-derive it:
+`grep -rhoE 'Common::[a-zA-Z_]+' plugins/Terminal/` and expect `Common::execute` to be missing.
+
+`docs/security-notes.md` §2 S-7 covers disabling `exec`/`proc_open`, which would neutralise **both**
+this plugin and the macros. That is the correct lever if you ever expose this container.
+
+---
+
+## 3. 🟠 The Macro dialog crashed when folder-scoped macros existed
+
+**Symptom:** the Settings → Macro dialog returned HTTP 500.
+
+**Root cause — invalid data by Atheos's own design.** `components/macro/dialog.php:35` does:
+
+```php
+implode(", ", $macro["fTypes"])     // requires an ARRAY
+```
+
+but `components/macro/class.macro.php` `save()` writes the **string** `"N/A"` for folder macros:
+
+```php
+"fTypes" => $type === "file" ? explode(",", $fTypes) : "N/A",
+```
+
+So **any folder-type macro** makes that dialog fatal:
+
+```
+PHP Fatal error: Uncaught TypeError: implode(): Argument #2 ($array) must be of type ?array,
+string given in /var/www/atheos/components/macro/dialog.php:35
+```
+
+**Fix applied — correct the DATA, not Atheos's code.** The stored `fTypes` for folder macros is now
+`[]` (an empty array) instead of `"N/A"`:
+
+```sh
+sed -i 's/"fTypes": "N\/A"/"fTypes": []/g' /var/www/atheos/data/macros.db.php
+```
+
+Verified: `implode()` now succeeds for all 8 macros.
+
+**Why data rather than code:** patching `dialog.php` would be overwritten by `update-atheos.sh`
+(and by any Atheos update), whereas valid data keeps working. The trade-off is that the UI's own
+"save" path could re-introduce `"N/A"` if a macro is edited in the UI — see the follow-up below.
+
+**Follow-up (not done):** the real upstream fix is
+`$type === "file" ? explode(",", $fTypes) : []` in `class.macro.php::save()`. Applying it would stop
+the UI re-introducing the bad value, at the cost of a patch that must be re-applied after updates.
+Worth doing if the dialog starts 500-ing again after editing a macro in the UI.
+
+---
+
+## 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
+verified working:
+
+```
+plugins.min.js contains 'plugins/Terminal/init.js'   -> YES   (bundle is fine)
+rightbar HTML                                        -> <a onclick="atheos.Terminal.open();">
+                                                        <i class="fas fa-terminal"></i>Terminal</a>
+```
+
+So when a plugin misbehaves, check in this order:
+
+```sh
+# 1. did it install?
+tail /var/www/atheos/data/log/market.log.php
+
+# 2. is its JS in the served bundle?
+grep -c "plugins/<Name>/init.js" /var/www/atheos/public/plugins.min.js
+
+# 3. is it a stale-API port? (Codiad-era plugins are the risk)
+grep -rhoE 'Common::[a-zA-Z_]+' /var/www/atheos/plugins/<Name>/ | sort -u
+#    then check each exists:  grep -rn "function <name>" /var/www/atheos/common.php /var/www/atheos/traits/
+
+# 4. is there a PHP fatal?
+grep -E 'PHP Fatal' /var/log/nginx/atheos.error.log | tail
+```
+
+**Rule of thumb:** if a plugin was ported from Codiad, assume its `Common::` calls are stale and
+verify them before trusting it.
+
+---
+
+## 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.
+
+### 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.
+
+### 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:
+
+```
+components/codegit/*      → Common::safe_execute  (31 call sites — every git operation)
+components/macro/*        → Common::raw_execute   (1 call site)
+common.php raw_execute    → function_exists("system") / function_exists("exec")
+```
+
+Every git commit, push, fetch and status from the editor goes through `exec`/`system`. Disabling them
+turns the editor into a text editor that cannot commit. So it stays **a deliberate exposure lever**
+(S-7 in `docs/security-notes.md`), to be applied only when the container is exposed — at which point
+you would also lose macros and git integration, which is why S-7 already says *"test, do not
+blind-apply"*.
+
+### 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.
+
+### 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.
+
+### 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 -----------------------------------------------------------------
-    # The socket path here MUST byte-match the pool's `listen =` in
-    #   /etc/php83/php-fpm.d/www.conf
-    # (interface I-1 — a mismatch yields a bare 502 with no other diagnostic).
+    # --- PHP: the socket path here MUST byte-match the pool's `listen =`
+    #     in /etc/php83/php-fpm.d/www.conf  (interface I-1 -> else bare 502)
     location ~ \.php$ {
         try_files $uri =404;
         fastcgi_split_path_info ^(.+\.php)(/.+)$;
@@ -27,11 +26,12 @@ server {
         try_files $uri $uri/ =404;
     }
 
-    # --- hardening -----------------------------------------------------------
-    location ~ /\.git  { deny all; }
-    location ~ /\.ssh  { deny all; }
-    location ~ /\.      { deny all; }
-    location ~ ^/data/ { deny all; }
+    # --- 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; }
+    location ~ ^/data/      { deny all; }
     location ~ ^/(config\.php|common\.php|controller\.php|traits/) { deny all; }
     location ~* \.(md|py|sh|log|conf|ini|sql|bak|orig)$ { 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;
+    }
 }

files/macros.db.php

@@ -25,7 +25,7 @@
         "uuid": "macro-writer-0001-start",
         "title": "1. Start/Join Writer Branch",
         "type": "folder",
-        "fTypes": "N/A",
+        "fTypes": [],
         "command": "cd %PATH% && (git checkout atheos-writer 2>/dev/null || git checkout -b atheos-writer) && git push -u origin atheos-writer",
         "icon": "fas fa-code-branch",
         "owner": "armistace"
@@ -34,7 +34,7 @@
         "uuid": "macro-writer-0002-commit",
         "title": "2. Commit + Push Writer Branch",
         "type": "folder",
-        "fTypes": "N/A",
+        "fTypes": [],
         "command": "cd %PATH% && (git config --get user.email >/dev/null || { echo 'ERROR: no git identity set. Run over SSH:  git config --global user.name \"Your Name\" && git config --global user.email \"you@example.com\"   (RUNBOOK STEP 1)'; exit 1; }) && git add -A && (git diff --cached --quiet || git commit -m \"writer: $(date +%F_%H%M)\") && git push origin atheos-writer",
         "icon": "fas fa-cloud-upload-alt",
         "owner": "armistace"
@@ -43,7 +43,7 @@
         "uuid": "macro-writer-0003-reset",
         "title": "3. DESTRUCTIVE: Reset Writer Branch to Master",
         "type": "folder",
-        "fTypes": "N/A",
+        "fTypes": [],
         "command": "cd %PATH% && git fetch origin && git reset --hard origin/master && git push --force-with-lease origin atheos-writer",
         "icon": "fas fa-exclamation-triangle",
         "owner": "armistace"
@@ -52,7 +52,7 @@
         "uuid": "macro-writer-0004-status",
         "title": "4. Status + Recent Log",
         "type": "folder",
-        "fTypes": "N/A",
+        "fTypes": [],
         "command": "cd %PATH% && git status --short --branch && echo '--- recent commits:' && git log --oneline -8 && echo '--- local branches:' && git branch",
         "icon": "fas fa-info-circle",
         "owner": "armistace"
@@ -61,7 +61,7 @@
         "uuid": "macro-writer-0005-refresh",
         "title": "5. Refresh Master (ff-only)",
         "type": "folder",
-        "fTypes": "N/A",
+        "fTypes": [],
         "command": "cd %PATH% && git checkout master && git pull --ff-only && git checkout atheos-writer",
         "icon": "fas fa-sync-alt",
         "owner": "armistace"
@@ -70,7 +70,7 @@
         "uuid": "macro-writer-0006-pullmaster",
         "title": "6. Merge Master Into Writer Branch",
         "type": "folder",
-        "fTypes": "N/A",
+        "fTypes": [],
         "command": "cd %PATH% && (git config --get user.email >/dev/null || { echo 'ERROR: no git identity set. Run over SSH:  git config --global user.name \"Your Name\" && git config --global user.email \"you@example.com\"   (RUNBOOK STEP 1)'; exit 1; }) && git fetch origin && git merge origin/master -m \"merge master into atheos-writer\" && git push origin atheos-writer",
         "icon": "fas fa-code-merge",
         "owner": "armistace"

patches/helpers-rDelete-GLOB_BRACE.diff

@@ -0,0 +1,22 @@
+--- /var/www/atheos/traits/helpers.php.orig
++++ /var/www/atheos/traits/helpers.php
+@@ -135,7 +135,18 @@
+ 
+         if (is_dir($target)) {
+ 
+-            $files = glob($target . "{*,.[!.]*,..?*}", GLOB_BRACE|GLOB_MARK); //GLOB_MARK adds a slash to directories returned
++            // GLOB_BRACE is a glibc extension and is UNDEFINED under musl (Alpine), where
++            // referencing it is a fatal error in PHP 8. Expand the brace pattern by hand
++            // so this works on both libcs.
++            if (defined("GLOB_BRACE")) {
++                $files = glob($target . "{*,.[!.]*,..?*}", GLOB_BRACE | GLOB_MARK);
++            } else {
++                $files = array_merge(
++                    glob($target . "/*", GLOB_MARK) ?: [],
++                    glob($target . "/.[!.]*", GLOB_MARK) ?: [],
++                    glob($target . "/..?*", GLOB_MARK) ?: []
++                );
++            }
+             // $files = glob($target . "/*");
+ 
+             foreach ($files as $file) {

scripts/build-and-test.sh

@@ -108,7 +108,49 @@ done
 
 echo
 echo "=============================================================="
-echo "GUARD: is master PROTECTED on the blog repo? (the writer-branch model depends on it)"
+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 "$PNL" | grep -oE 'height:[^;]*' | head -1))"
+fi
+# and the CSS/JS cache header must be present, or fixes stay invisible
+if wget -qO /dev/null --server-response --header='Host: 127.0.0.1' http://127.0.0.1/theme/main.min.css 2>&1 | grep -qi 'Cache-Control.*no-cache'; then
+  ok "theme CSS sends Cache-Control: no-cache (changes are picked up)"
+else
+  bad "theme CSS has no Cache-Control - a CSS fix can stay hidden behind the browser cache"
+fi
+echo
+echo "=============================================================="
+echo "REGRESSION: rDelete works (GLOB_BRACE is glibc-only; musl lacks it)"
+echo "=============================================================="
+# That broke deleting ANY file/folder in the editor AND removing a market plugin (the UI
+# would spin forever because the fatal killed the response before Common::send()).
+# docs/known-issues.md §1. This test fails loudly if the patch is lost (e.g. by an update).
+rm -rf /tmp/rdel_guard 2>/dev/null
+if mkdir -p /tmp/rdel_guard/a/b/c /tmp/rdel_guard/.hd 2>/dev/null \
+   && touch /tmp/rdel_guard/f.txt /tmp/rdel_guard/.dot /tmp/rdel_guard/a/b/c/deep.txt; then
+  ROUT=$(php83 -r 'require_once("/var/www/atheos/common.php"); echo Common::rDelete("/tmp/rdel_guard/") ? "ok" : "fail";' 2>&1 | grep -viE 'deprecat|warning|notice' | tail -1)
+  if [ "$ROUT" = "ok" ] && [ ! -e /tmp/rdel_guard ]; then
+    ok "rDelete removed a nested tree incl. dotfiles (delete works)"
+  else
+    if echo "$ROUT" | grep -q 'GLOB_BRACE'; then
+      bad "rDelete FATALS on GLOB_BRACE - re-apply patches/helpers-rDelete-GLOB_BRACE.diff"
+    else
+      bad "rDelete failed (got: $ROUT)"
+    fi
+  fi
+else
+  bad "could not build the rDelete test tree"
+fi
+rm -rf /tmp/rdel_guard 2>/dev/null
 echo "=============================================================="
 # The whole branch-based workflow assumes the deploy key CANNOT push master. That is a
 # repo-side setting we cannot verify from here by inspection - so test it the way an
@@ -128,10 +170,22 @@ fi
 
 echo
 echo "=============================================================="
-echo "FR-11 GUARD: agent created NO identity or armistace credential"
+echo "IDENTITY: git identity is SET by the operator (FR-11 superseded by explicit request)"
 echo "=============================================================="
-chk "git user.name empty"  "$(asuser 'git config --get user.name'  2>/dev/null)" ""
-chk "git user.email empty" "$(asuser 'git config --get user.email' 2>/dev/null)" ""
+# FR-11 originally required the agent to leave the identity EMPTY so it could not impersonate
+# the operator. The operator has since explicitly asked for it to be set, so the requirement is
+# superseded - and the guard is inverted: the identity must now be present and must be the
+# OPERATOR's, not an agent-invented one. Guarding the old expectation would assert the opposite
+# of the current design and fail forever (which is what it did).
+NAME=$(asuser 'git config --get user.name'  2>/dev/null)
+MAIL=$(asuser 'git config --get user.email' 2>/dev/null)
+if [ -n "$NAME" ]; then ok "git user.name set ($NAME)"; else bad "git user.name is empty - macro 2 will refuse to commit"; fi
+if [ -n "$MAIL" ]; then ok "git user.email set ($MAIL)"; else bad "git user.email is empty"; fi
+case "$MAIL" in
+  *hermes*|*bot*|*noreply@anthropic*|*agent*) bad "identity looks agent-generated: $MAIL" ;;
+  "") ;;
+  *) ok "identity is an operator address, not an agent-invented one" ;;
+esac
 if [ -f /home/atheos/.ssh/id_ed25519_blog ]; then ok "deploy key present"; else bad "deploy key missing"; fi
 chk "deploy key mode" "$(stat -c '%a' /home/atheos/.ssh/id_ed25519_blog 2>/dev/null)" "600"
 chk "deploy key owner" "$(stat -c '%U' /home/atheos/.ssh/id_ed25519_blog 2>/dev/null)" "atheos"

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 ==="