Codex installer: findNextTableHeader skips past [[array-of-tables]], silently deleting sibling [[...]] blocks in ~/.codex/config.toml on install/upgrade/uninstall — verified

[inth3shadows]

Summary

The Codex installer's TOML block finder, findNextTableHeader in src/installer/targets/toml.ts, skips past [[array-of-tables]] headers instead of treating them as a boundary when locating the end of the [mcp_servers.codegraph] block. As a result, any [[...]] block located after the codegraph table in ~/.codex/config.toml is treated as part of the codegraph block and is silently deleted — on uninstall (removeTomlTable), and on install/upgrade when the block is rewritten (upsertTomlTable's replaced path). This contradicts the module's own doc comment ("Everything outside that block is preserved verbatim, byte-for-byte") and the intended invariant that sibling [[array_of_tables]] blocks survive. Verified against the real exported helpers that codex.ts calls.

Root cause

// src/installer/targets/toml.ts:140-154
function findNextTableHeader(content: string, from: number): number {
  // Look for "\n[" but skip "\n[[" (array of tables).
  let i = from;
  while (i < content.length) {
    const nlIdx = content.indexOf('\n[', i);
    if (nlIdx === -1) return content.length;
    if (content[nlIdx + 2] === '[') {
      // [[...]] — keep searching past it.
      i = nlIdx + 2;      // <- skips the array-of-tables header instead of stopping at it
      continue;
    }
    return nlIdx + 1;
  }
  return content.length;
}

Because \n[[ is skipped rather than treated as the end of the current block, blockEnd runs to EOF (or to the next single-bracket table), so everything from the codegraph header through the trailing [[...]] block is considered the codegraph block. removeTomlTable (toml.ts:116-120) and upsertTomlTable's replace branch (toml.ts:82-101) then drop that range.

Both are on the real Codex install/uninstall path: src/installer/targets/codex.ts:102 calls removeTomlTable on uninstall, and codex.ts:155 calls upsertTomlTable on install/upgrade.

Repro (executed against the real exported helpers)

import { removeTomlTable, upsertTomlTable, buildTomlTable }
  from './dist/installer/targets/toml.js';

const file = `[mcp_servers.codegraph]
command = "codegraph"
args = ["serve", "--mcp"]

[[history]]
id = 1
note = "must survive"
`;

removeTomlTable(file, 'mcp_servers.codegraph');
// => { content: "", action: "removed" }        // the entire [[history]] block is gone

const newBlock = buildTomlTable('mcp_servers.codegraph',
  { command: 'codegraph', args: ['serve','--mcp','--v2'] });
upsertTomlTable(file, 'mcp_servers.codegraph', newBlock);
// => { content: '[mcp_servers.codegraph]\ncommand = "codegraph"\nargs = ["serve", "--mcp", "--v2"]\n',
//      action: "replaced" }                     // [[history]] dropped on the upgrade rewrite too

Expected: the [[history]] block is preserved (uninstall should leave [[history]] behind; upgrade should keep it below the rewritten codegraph table).

Suggested direction

findNextTableHeader should treat a \n[[ as a boundary too (stop there) — any new table header, single- or double-bracket, ends the current block. There is currently no test covering a sibling [[array-of-tables]] block in installer-targets.test.ts; a Codex fixture with a trailing [[...]] across install → upgrade-reinstall → uninstall would pin it.

Environment

main @ 2d72891, package 1.4.1, Node 22.23.1 (Linux). Reproduces on a clean npm ci && npm run build.

[inth3shadows]

Suggested label for triage (I lack permission to apply it myself): bug.