# 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".

> **⚠️ Superseded by §6.** This section fixed a real layout bug, but it was NOT the cause of the
> empty CodeGit dialog. The actual cause was a relative project path making the request 403, which
> the modal silently swallowed. Both are fixed; if a dialog is ever blank again, read §6 first.

**This was NOT a codegit bug in the JS sense.** 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 in §4 looked
like it had not worked at all. Reported twice, the second time with "is it because I'm on Firefox?"

**It was not Firefox.** Verified in a real, scripted Firefox (155.0) against the live server with the
fix applied:

```
assets Firefox requested:  theme/main.min.css?v=1790663824   <- versioned
applied panel rule:        height: auto; max-height: 58vh    <- the fix
dialog 193px | panel 138px | toolbar INSIDE | JS errors: none
```

The panel rendered correctly and the Branch toolbar sat inside the modal. Firefox behaves identically
to Chromium here; it was simply still running the **old cached stylesheet**.

**Root cause — stable asset URLs, with nothing to bust them.** Atheos emits:

```html
<link rel="stylesheet" href="theme/main.min.css">   <!-- no version -->
<script src="public/modules.min.js"></script>       <!-- no version -->
```

Same path before and after a change, and originally no cache headers at all. A browser therefore keeps
its cached copy across an update, and never even asks the server. Changing the CSS on the server
cannot fix that — the browser is not fetching it.

**Fix (two parts):**

1. **nginx** sends `Cache-Control: no-cache, must-revalidate` for `*.css`/`*.js`. This does **not**
   disable caching — it forces **revalidation**, so normal loads still get a cheap 304 while changes
   are picked up.
2. **Versioned URLs.** `SourceManager::getTag()` and the theme link in `index.php` now append the
   file's mtime (`?v=<mtime>`). A changed file gets a **new URL** so it is fetched immediately; an
   unchanged file keeps its URL and stays cached.

Part 2 is the one that actually mattered here: it works **even against an already-poisoned cache**,
which part 1 alone cannot do. Once the *page* refreshes (it is served `no-store`), every asset URL it
references is new, so the stale CSS is bypassed with no manual clearing.

**If you ever see a stale UI again:** force a reload (Ctrl/Cmd-Shift-R). If that fixes it, this
section is why.

**Forcing this one time:** if a browser holds an old copy, any of these work —
Ctrl/Cmd-Shift-R, `about:blank` then back, a private window, or `rm -rf` the profile's cache. Or just
change the file's mtime (`touch`) and the URL changes by itself.

---

## 6. 🔴 Every dialog rendered EMPTY (CodeGit "just a black box")

**Symptom:** CodeGit — and, it turns out, the Macro / Market / Settings dialogs — opened as an empty
black area. No error, no text, nothing. Reported as *"codegit still no go just a black box"*, twice,
and it survived the CSS fix in §4, because it was never a CSS problem.

**This is the bug that actually mattered.** §4 and §5 were real defects, but neither was the cause.

### The chain

1. **The installer stores a RELATIVE path.** `components/install/process.php` keeps the folder name
   as given, so the project store held `{"Blog": "blog"}` — not an absolute path.
2. **`loadState()` hands it to the UI unmodified and persists it** (`common.php`):

   ```php
   $projectPath = reset($projectList);          // "blog"
   ...
   SESSION("projectPath", $projectPath);        // stored -> the bad value STICKS across logins
   ```

3. **The file tree puts it straight into the DOM** (`components/filetree/init.js`):

   ```js
   let path = atheos.current.projectPath;
   `<a id="project-root" data-type="root" data-path="${path}">`   // data-path="blog"
   ```

4. **CodeGit then sends `repo="blog"`**, and `getWorkspacePath("blog")` fails its access check:

   ```
   traits/path.php:67   Common::send(403, "Client does not have access.");
   ```

5. **`modal.js` silently discards the failure** — this is what makes it look like a "black box"
   rather than an error:

   ```js
   settled: function(reply, status) {
       if (status !== 200) return;      // no message, no toast, no console error
       content.html(reply);
   ```

So the request 403s, nothing is rendered, and nothing is reported. The dialog is left with an empty
`<section id="content">`.

### How it was pinned down

Not by reading CSS. By capturing the real request/response from a scripted browser:

```
POST /dialog.php   {"target":"codegit","action":"codegit","repo":"blog"}
-> 403  (and #content innerHTML length: 0)
```

A relative path was reproduced directly:

```
is_dir("blog") from the app root        -> NO
getWorkspacePath("blog")                -> 403 Client does not have access.
projects store                          -> {"Blog": "blog"}
```

### Fix (`scripts/fix-project-path.sh`)

A relative value in the store is **legitimate** — Atheos's own project-creation code resolves
relative → `WORKSPACE/<name>`. `loadState()` simply never does. Two changes, both required:

**A. Resolve at load time, and re-store it** — this heals sessions already holding the bad value:

```php
if (!Common::isAbsPath($projectPath)) {
    $projectPath = Common::getWorkspacePath($projectPath, true);
    SESSION("projectPath", $projectPath);
}
```

**B. Make the store absolute** (`{"Blog": "/var/www/atheos/workspace/blog"}`) so that
`array_search($projectPath, $projectList)`, which `loadState()` uses to derive the project *name*
for the tree label, keeps working. Fixing only (A) would silently break the label — the path would
resolve but `array_search` would return `false`, so the tree would show an empty name.

**Verified** by starting from a deliberately poisoned session (`projectPath="blog"`) and confirming
it self-heals:

```
projectPath : /var/www/atheos/workspace/blog    <- healed from "blog"
data-path   : /var/www/atheos/workspace/blog
dialog.php  : 200 with content
#content    : 1758 chars
visible     : CodeGit Overview Log Transfer Configure Commit Amend ...
```

**An existing browser session heals on its next page load** — no hard refresh or re-login needed.

### Worth remembering

A 403 from `getWorkspacePath()` presents as *"the dialog is empty"*, with no error anywhere. If any
Atheos dialog is ever blank again, check the **project path** first, then the response code — not the CSS.

---

## 7. 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.

---

## 8. 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.

### 8.0 Branch protection on `master` — ACCEPTED RISK

Deliberately **not** enabled while the editor is LAN-only (operator decision). Full reasoning and the
"enable it before you expose this host" trigger are in
[`docs/writer-branch-workflow.md` §2](writer-branch-workflow.md#2-protect-master-on-the-blog-repo--recommendation-deliberately-not-enabled).

The suite still probes for it on every run and reports `ACCEPTED-RISK` (not a failure) while it is
off, so the recommendation self-cancels the moment it is enabled.

### 8.1 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.

### 8.2 ❌ `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"*.

### 8.3 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.

### 8.4 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.

### 8.5 The real upstream fix for §3

`class.macro.php::save()` should write `[]` instead of `"N/A"` for folder macros. See §4 — the fix is
currently applied to the data, so it survives updates, at the cost of being reversible from the UI.