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fix(codex-runtime): keep migrated root keys top-level#25857

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steezkelly:fix/codex-runtime-toml-root
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fix(codex-runtime): keep migrated root keys top-level#25857
steezkelly wants to merge 1 commit into
NousResearch:mainfrom
steezkelly:fix/codex-runtime-toml-root

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@steezkelly

@steezkelly steezkelly commented May 14, 2026

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Summary

  • Inserts the Hermes-managed Codex runtime block before the first TOML table when migrating ~/.codex/config.toml
  • Keeps default_permissions = ":workspace" as a true top-level key instead of accidentally nesting it under [features] / [projects]
  • Adds a regression test that parses the generated TOML and verifies the key placement

Why

If an existing Codex config ended in a table, appending the managed block caused Codex to parse default_permissions as table-scoped (for example features.default_permissions). Codex then failed startup with:

invalid type: string ":workspace", expected a boolean

Test Plan

  • /home/steve/.hermes/hermes-agent/venv/bin/python -m pytest tests/hermes_cli/test_codex_runtime_plugin_migration.py -q -o addopts=''
  • git diff --check

@alt-glitch alt-glitch added type/bug Something isn't working P2 Medium — degraded but workaround exists comp/cli CLI entry point, hermes_cli/, setup wizard labels May 14, 2026
@kshitijk4poor kshitijk4poor mentioned this pull request May 15, 2026
Merged
kshitijk4poor added a commit to kshitijk4poor/hermes-agent that referenced this pull request May 15, 2026
@kshitijk4poor
fix(codex-runtime): de-dup [plugins.X] tables and stop leaking HERMES…
7ab5aee 
…_HOME into config.toml

Builds on @steezkelly's Bug A fix (NousResearch#25857, top-level default_permissions
via _insert_managed_block_at_top_level) by addressing the other two
config-corruption bugs described in NousResearch#26250:

Bug B (duplicate [plugins.X] tables)
  - Codex itself writes [plugins."<name>@<marketplace>"] tables to
    config.toml when the user runs `codex plugins enable` directly,
    before hermes-agent's managed block exists. On the next migrate run,
    _query_codex_plugins() re-discovers the same plugins via plugin/list
    and render_codex_toml_section() re-emits them inside the managed
    block. Codex's strict TOML parser then rejects the duplicate table
    header on startup.
  - Add _strip_unmanaged_plugin_tables() that drops [plugins.*] tables
    from the user-content portion of the file. Only run it when
    plugin/list succeeded — if the RPC failed we can't re-emit and
    must preserve the user's tables. plugin/list is the source of
    truth when it answers.

Bug C (HERMES_HOME pytest-tempdir leak into ~/.codex/config.toml)
  - _build_hermes_tools_mcp_entry() read HERMES_HOME directly from
    os.environ, so a sibling pytest's monkeypatch.setenv("HERMES_HOME",
    tmp_path) silently burned a transient pytest tempdir into the
    user's real ~/.codex/config.toml. After pytest reaped the tempdir,
    every codex-routed hermes-tools tool call failed silently.
  - Derive HERMES_HOME from get_hermes_home() (the canonical resolver
    that goes through the profile-aware path) and refuse to emit
    obvious test-tempdir paths via _looks_like_test_tempdir() as
    belt-and-suspenders for any other callsite that forgets to patch
    migrate().
  - test_enable_succeeds_when_codex_present in test_codex_runtime_switch.py
    invoked the real migrate() (no mock), writing to Path.home() / .codex
    using whatever HERMES_HOME the running pytest session had set. Add
    the same migrate patch the other apply() tests already use, so the
    suite stops touching the user's real ~/.codex/config.toml.

E2E verification (replicating the issue's repro):
  - Pre-state config.toml with user [mcp_servers.omx_team_run] +
    codex-installed [plugins."tasks@openai-curated"],
    HERMES_HOME="/private/var/folders/.../pytest-of-.../..."
  - On origin/main: tomllib refuses to load the result with
    "Cannot declare ('plugins', 'tasks@openai-curated') twice" AND
    the pytest-tempdir HERMES_HOME is burned in.
  - On this branch: file parses cleanly, default_permissions is
    top-level, exactly one [plugins."tasks@openai-curated"] table
    inside the managed block, no HERMES_HOME in the MCP env.

7 new regression tests covering all three bugs + the test-leak guard.
`bash scripts/run_tests.sh tests/hermes_cli/test_codex_runtime_*.py` —
95 passed, 0 failed.

Closes NousResearch#26250
kshitijk4poor added a commit that referenced this pull request May 15, 2026
@kshitijk4poor
fix(codex-runtime): de-dup [plugins.X] tables and stop leaking HERMES…
7727607 
…_HOME into config.toml

Builds on @steezkelly's Bug A fix (#25857, top-level default_permissions
via _insert_managed_block_at_top_level) by addressing the other two
config-corruption bugs described in #26250:

Bug B (duplicate [plugins.X] tables)
  - Codex itself writes [plugins."<name>@<marketplace>"] tables to
    config.toml when the user runs `codex plugins enable` directly,
    before hermes-agent's managed block exists. On the next migrate run,
    _query_codex_plugins() re-discovers the same plugins via plugin/list
    and render_codex_toml_section() re-emits them inside the managed
    block. Codex's strict TOML parser then rejects the duplicate table
    header on startup.
  - Add _strip_unmanaged_plugin_tables() that drops [plugins.*] tables
    from the user-content portion of the file. Only run it when
    plugin/list succeeded — if the RPC failed we can't re-emit and
    must preserve the user's tables. plugin/list is the source of
    truth when it answers.

Bug C (HERMES_HOME pytest-tempdir leak into ~/.codex/config.toml)
  - _build_hermes_tools_mcp_entry() read HERMES_HOME directly from
    os.environ, so a sibling pytest's monkeypatch.setenv("HERMES_HOME",
    tmp_path) silently burned a transient pytest tempdir into the
    user's real ~/.codex/config.toml. After pytest reaped the tempdir,
    every codex-routed hermes-tools tool call failed silently.
  - Derive HERMES_HOME from get_hermes_home() (the canonical resolver
    that goes through the profile-aware path) and refuse to emit
    obvious test-tempdir paths via _looks_like_test_tempdir() as
    belt-and-suspenders for any other callsite that forgets to patch
    migrate().
  - test_enable_succeeds_when_codex_present in test_codex_runtime_switch.py
    invoked the real migrate() (no mock), writing to Path.home() / .codex
    using whatever HERMES_HOME the running pytest session had set. Add
    the same migrate patch the other apply() tests already use, so the
    suite stops touching the user's real ~/.codex/config.toml.

E2E verification (replicating the issue's repro):
  - Pre-state config.toml with user [mcp_servers.omx_team_run] +
    codex-installed [plugins."tasks@openai-curated"],
    HERMES_HOME="/private/var/folders/.../pytest-of-.../..."
  - On origin/main: tomllib refuses to load the result with
    "Cannot declare ('plugins', 'tasks@openai-curated') twice" AND
    the pytest-tempdir HERMES_HOME is burned in.
  - On this branch: file parses cleanly, default_permissions is
    top-level, exactly one [plugins."tasks@openai-curated"] table
    inside the managed block, no HERMES_HOME in the MCP env.

7 new regression tests covering all three bugs + the test-leak guard.
`bash scripts/run_tests.sh tests/hermes_cli/test_codex_runtime_*.py` —
95 passed, 0 failed.

Closes #26250
@kshitijk4poor

kshitijk4poor commented May 15, 2026

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Thanks for the thorough fix @steezkelly — Bug A landed via #26260 with your commit cherry-picked, authorship preserved. That PR also addresses the two sibling bugs in the same issue (#26250):

  • Bug B — codex's pre-existing [plugins."<name>@<marketplace>"] tables outside the managed block colliding with the ones we re-emit inside it (duplicate-table-header parse error).
  • Bug C — HERMES_HOME leaking from os.environ into ~/.codex/config.toml when pytest sets a tempdir, plus the test-suite leak that triggered the original report.

Closing as merged via #26260. Thanks again.

@briandevans briandevans mentioned this pull request May 15, 2026
Closed
6 tasks
DIZ-admin pushed a commit to DIZ-admin/hermes-agent that referenced this pull request May 16, 2026
@kshitijk4poor @hermes-agent
fix(codex-runtime): de-dup [plugins.X] tables and stop leaking HERMES…
4051a9c 
…_HOME into config.toml

Builds on @steezkelly's Bug A fix (NousResearch#25857, top-level default_permissions
via _insert_managed_block_at_top_level) by addressing the other two
config-corruption bugs described in NousResearch#26250:

Bug B (duplicate [plugins.X] tables)
  - Codex itself writes [plugins."<name>@<marketplace>"] tables to
    config.toml when the user runs `codex plugins enable` directly,
    before hermes-agent's managed block exists. On the next migrate run,
    _query_codex_plugins() re-discovers the same plugins via plugin/list
    and render_codex_toml_section() re-emits them inside the managed
    block. Codex's strict TOML parser then rejects the duplicate table
    header on startup.
  - Add _strip_unmanaged_plugin_tables() that drops [plugins.*] tables
    from the user-content portion of the file. Only run it when
    plugin/list succeeded — if the RPC failed we can't re-emit and
    must preserve the user's tables. plugin/list is the source of
    truth when it answers.

Bug C (HERMES_HOME pytest-tempdir leak into ~/.codex/config.toml)
  - _build_hermes_tools_mcp_entry() read HERMES_HOME directly from
    os.environ, so a sibling pytest's monkeypatch.setenv("HERMES_HOME",
    tmp_path) silently burned a transient pytest tempdir into the
    user's real ~/.codex/config.toml. After pytest reaped the tempdir,
    every codex-routed hermes-tools tool call failed silently.
  - Derive HERMES_HOME from get_hermes_home() (the canonical resolver
    that goes through the profile-aware path) and refuse to emit
    obvious test-tempdir paths via _looks_like_test_tempdir() as
    belt-and-suspenders for any other callsite that forgets to patch
    migrate().
  - test_enable_succeeds_when_codex_present in test_codex_runtime_switch.py
    invoked the real migrate() (no mock), writing to Path.home() / .codex
    using whatever HERMES_HOME the running pytest session had set. Add
    the same migrate patch the other apply() tests already use, so the
    suite stops touching the user's real ~/.codex/config.toml.

E2E verification (replicating the issue's repro):
  - Pre-state config.toml with user [mcp_servers.omx_team_run] +
    codex-installed [plugins."tasks@openai-curated"],
    HERMES_HOME="/private/var/folders/.../pytest-of-.../..."
  - On origin/main: tomllib refuses to load the result with
    "Cannot declare ('plugins', 'tasks@openai-curated') twice" AND
    the pytest-tempdir HERMES_HOME is burned in.
  - On this branch: file parses cleanly, default_permissions is
    top-level, exactly one [plugins."tasks@openai-curated"] table
    inside the managed block, no HERMES_HOME in the MCP env.

7 new regression tests covering all three bugs + the test-leak guard.
`bash scripts/run_tests.sh tests/hermes_cli/test_codex_runtime_*.py` —
95 passed, 0 failed.

Closes NousResearch#26250
@1960697431 1960697431 mentioned this pull request May 17, 2026
Open
@Vodkakakaka Vodkakakaka mentioned this pull request May 23, 2026
Open
gweeteve pushed a commit to gweeteve/hermes-agent that referenced this pull request Jun 2, 2026
@kshitijk4poor
fix(codex-runtime): de-dup [plugins.X] tables and stop leaking HERMES…
db66535 
…_HOME into config.toml

Builds on @steezkelly's Bug A fix (NousResearch#25857, top-level default_permissions
via _insert_managed_block_at_top_level) by addressing the other two
config-corruption bugs described in NousResearch#26250:

Bug B (duplicate [plugins.X] tables)
  - Codex itself writes [plugins."<name>@<marketplace>"] tables to
    config.toml when the user runs `codex plugins enable` directly,
    before hermes-agent's managed block exists. On the next migrate run,
    _query_codex_plugins() re-discovers the same plugins via plugin/list
    and render_codex_toml_section() re-emits them inside the managed
    block. Codex's strict TOML parser then rejects the duplicate table
    header on startup.
  - Add _strip_unmanaged_plugin_tables() that drops [plugins.*] tables
    from the user-content portion of the file. Only run it when
    plugin/list succeeded — if the RPC failed we can't re-emit and
    must preserve the user's tables. plugin/list is the source of
    truth when it answers.

Bug C (HERMES_HOME pytest-tempdir leak into ~/.codex/config.toml)
  - _build_hermes_tools_mcp_entry() read HERMES_HOME directly from
    os.environ, so a sibling pytest's monkeypatch.setenv("HERMES_HOME",
    tmp_path) silently burned a transient pytest tempdir into the
    user's real ~/.codex/config.toml. After pytest reaped the tempdir,
    every codex-routed hermes-tools tool call failed silently.
  - Derive HERMES_HOME from get_hermes_home() (the canonical resolver
    that goes through the profile-aware path) and refuse to emit
    obvious test-tempdir paths via _looks_like_test_tempdir() as
    belt-and-suspenders for any other callsite that forgets to patch
    migrate().
  - test_enable_succeeds_when_codex_present in test_codex_runtime_switch.py
    invoked the real migrate() (no mock), writing to Path.home() / .codex
    using whatever HERMES_HOME the running pytest session had set. Add
    the same migrate patch the other apply() tests already use, so the
    suite stops touching the user's real ~/.codex/config.toml.

E2E verification (replicating the issue's repro):
  - Pre-state config.toml with user [mcp_servers.omx_team_run] +
    codex-installed [plugins."tasks@openai-curated"],
    HERMES_HOME="/private/var/folders/.../pytest-of-.../..."
  - On origin/main: tomllib refuses to load the result with
    "Cannot declare ('plugins', 'tasks@openai-curated') twice" AND
    the pytest-tempdir HERMES_HOME is burned in.
  - On this branch: file parses cleanly, default_permissions is
    top-level, exactly one [plugins."tasks@openai-curated"] table
    inside the managed block, no HERMES_HOME in the MCP env.

7 new regression tests covering all three bugs + the test-leak guard.
`bash scripts/run_tests.sh tests/hermes_cli/test_codex_runtime_*.py` —
95 passed, 0 failed.

Closes NousResearch#26250
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@steezkelly @kshitijk4poor @alt-glitch