Every settings field declares its tier; a value in the wrong file is an error naming
file, key and tier. A field naming a program or affecting a gate cannot be declared
instance. Secrets are references only: {"ref": "<name>"} via WIKITOOL_SECRET_<NAME> or
a user-only secrets file, {"ref": "op://..."} via op read (locked 1Password: exit 42).
The preflight records op as an optional tool. doctor gains one line per tier, docs
verify checks a committed wikitool.json for plaintext secrets, CI resolves a real
op:// value through 1password/load-secrets-action. No feature reads its settings
this way yet; without the two files every other command is unchanged.
Files changed:
- .gitea/workflows/ci.yml
- .gitignore
- AGENTS.md
- CHANGES.md
- INSTALL.md
- VERSION
- docs/explanation/README.md
- docs/explanation/configuration-tiers.md
- docs/how-to/README.md
- docs/how-to/use-1password-for-settings.md
- docs/reference/commands/README.md
- docs/reference/commands/configuration.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/types-instructions-and-docs.md
- docs/reference/configuration.md
- docs/reference/exit-codes.md
- instructions/dev/doc-pull-through.md
- instructions/dev/testing-conventions.md
- instructions/preflight.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli.py
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/_util.py
- tools/chemenu/commands/config_cmd.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/config.py
- tools/chemenu/config_shapes.py
- tools/chemenu/prerequisites.py
- tools/chemenu/settings.py
- tools/chemenu/tests/conftest.py
- tools/chemenu/tests/test_dist_cmd.py
- tools/chemenu/tests/test_preflight.py
- tools/chemenu/tests/test_preflight_pwsh.py
- tools/chemenu/tests/test_settings.py
- tools/chemenu/toolpaths.py
- tools/preflight.ps1
- tools/preflight.sh
- tools/prerequisites.txt
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
A mail's text is its plain text unless that is under 10% of the HTML text, then the HTML text
with a warning; one rule for .eml and .msg. The other version of the text in a
multipart/alternative is no longer an attachment.
Files changed:
- CHANGES.md
- VERSION
- docs/reference/commands/raw-material-and-uploads.md
- testfiles/mail/gog-roundcube.eml.expect
- tools/CONTRACT.md
- tools/chemenu/commands/raw_cmd.py
- tools/chemenu/filters/mail.py
- tools/chemenu/filters/msg.py
- tools/chemenu/tests/test_raw_derive.py
- tools/chemenu/tests/test_raw_derive_binary.py
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
Each sheet becomes NN-<sheet>.tsv (RFC 4180, tab-delimited, A1-aligned) in a
<stem>.sheets/ folder beside the .md; sheets with formulas also get a
.formulas.tsv. derived.md is the overview. Adds testfiles/ with a CI test.
Files changed:
- .gitattributes
- CHANGES.md
- VERSION
- docs/dev/development.md
- docs/how-to/ingest-a-source.md
- docs/reference/commands/raw-material-and-uploads.md
- raw/CONTRACT.md
- testfiles/README.md
- tools/CONTRACT.md
- tools/chemenu/commands/raw_cmd.py
- tools/chemenu/filters/__init__.py
- tools/chemenu/filters/archive.py
- tools/chemenu/filters/ooxml.py
- tools/chemenu/tests/test_raw_derive.py
- tools/chemenu/tests/test_raw_derive_testfiles.py
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
A derived PDF is a folder since raw derive; the raw/CONTRACT.md example was
adapted when the command shipped, the raw pending record and its generated
copies were not.
Files changed:
- CHANGES.md
- VERSION
- docs/reference/commands/raw-material-and-uploads.md
- tools/CONTRACT.md
- tools/chemenu/commands/raw_cmd.py
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
PDF is read with pypdf (page markers, scan warning, encrypted files refused), Outlook .msg with olefile as a container like an .eml, and a .msg attached to a mail is quoted. Both packages are in tools/requirements.txt and imported only when such a file is derived, so a missing one stops that format alone. doctor reports one import-filter line per package-backed format.
Files changed:
- CHANGES.md
- VERSION
- docs/how-to/ingest-a-source.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/raw-material-and-uploads.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/commands/doctor.py
- tools/chemenu/commands/raw_cmd.py
- tools/chemenu/filters/__init__.py
- tools/chemenu/filters/mail.py
- tools/chemenu/filters/msg.py
- tools/chemenu/filters/pdf.py
- tools/chemenu/tests/binary_formats.py
- tools/chemenu/tests/test_raw_derive_binary.py
- tools/requirements.txt
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
A ZIP becomes incoming/<stem>/ with its files and a derived text beside each
document, the ZIP is removed and its sha256 named in the output. A mail with
attachments becomes a folder with original.eml, derived.md and the attachments;
a ZIP attached to a mail is unpacked once, an attached mail is quoted. Unsafe
entries, nested ZIPs and size limits are refused before anything is written.
Files changed:
- CHANGES.md
- VERSION
- docs/how-to/ingest-a-source.md
- docs/reference/commands/README.md
- docs/reference/commands/raw-material-and-uploads.md
- raw/CONTRACT.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/commands/raw_cmd.py
- tools/chemenu/filters/__init__.py
- tools/chemenu/filters/archive.py
- tools/chemenu/filters/mail.py
- tools/chemenu/tests/test_portability.py
- tools/chemenu/tests/test_raw_derive.py
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
Adds the import-filter registry (tools/chemenu/filters), the raw derive command with folder form,
path-budget and name checks, DOCX/PPTX/XLSX and EML filters, the pending and accept hints, the
wiki-ingest skill step and the raw/CONTRACT.md section. First of three cuts; containers and
PDF/MSG follow.
Files changed:
- CHANGES.md
- VERSION
- docs/how-to/ingest-a-source.md
- docs/reference/commands/README.md
- docs/reference/commands/raw-material-and-uploads.md
- instructions/wiki-ingest/SKILL.md
- raw/CONTRACT.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/raw_cmd.py
- tools/chemenu/filters/__init__.py
- tools/chemenu/filters/html_page.py
- tools/chemenu/filters/mail.py
- tools/chemenu/filters/ooxml.py
- tools/chemenu/tests/test_raw_derive.py
- tools/chemenu/web_capture.py
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
A part of the stack that will not move from the unpack folder into place is
retried for about 30 seconds; each retry removes what reached the target and
unpacks the entry afresh from the archive, so the entry ends up there once and
whole. If it still fails, both scripts take back everything they moved and exit 1
with the system's message and "nothing was installed". New test hook
CHEMENU_PREFLIGHT_MOVE_FAIL=<entry>:<n>[:partial].
Files changed:
- CHANGES.md
- INSTALL.md
- VERSION
- instructions/preflight.md
- tools/CONTRACT.md
- tools/chemenu/tests/conftest.py
- tools/chemenu/tests/test_preflight.py
- tools/chemenu/tests/test_preflight_pwsh.py
- tools/preflight.ps1
- tools/preflight.sh
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
The help and exit-42 cause texts still said "rebase-review gate" after the display
name was settled; the generated reference and CONTRACT row follow.
Files changed:
- CHANGES.md
- VERSION
- docs/reference/commands/git.md
- docs/reference/exit-codes.md
- tools/CONTRACT.md
- tools/chemenu/commands/git_publish.py
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
The gate list contradicted itself across AGENTS.md, instructions/gates.md and the
command records' gate names. The Rebase-Review Gate is now listed, `new project`'s
exit 42 is no longer a pseudo-gate, gates.md and the explanation page link to the one
list instead of counting, and a register plus a docs verify check keep the three in step.
Files changed:
- AGENTS.md
- CHANGES.md
- VERSION
- docs/explanation/why-gates-are-code.md
- docs/reference/commands/pages.md
- docs/reference/commands/types-instructions-and-docs.md
- docs/reference/exit-codes.md
- instructions/gates.md
- tools/CONTRACT.md
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/commands/git_publish.py
- tools/chemenu/commands/new_page.py
- tools/chemenu/errors.py
- tools/chemenu/mcp/server.py
- tools/chemenu/tests/test_cli_contract.py
- tools/chemenu/tests/test_docs_verify.py
- tools/chemenu/tests/test_git_publish.py
- tools/chemenu/tests/test_reference_doc.py
Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
The telemetry, remotes, upload and tasks loaders take field names, defaults, coercions and their Expected: text from the record and accept exactly what they did before. doctor WARNs on a telemetry file the policy silently reads differently. configuration.md carries one generated region per file, also checked in an instance. docs reference --apply now refreshes several regions in one page in sequence instead of keeping only the last.
Files changed:
- CHANGES.md
- VERSION
- docs/how-to/set-up-the-mcp-server.md
- docs/reference/README.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/types-instructions-and-docs.md
- docs/reference/configuration.md
- instructions/dev/doc-pull-through.md
- instructions/setup-instance.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/commands/git_publish.py
- tools/chemenu/config.py
- tools/chemenu/config_shapes.py
- tools/chemenu/reference_doc.py
- tools/chemenu/tasks/caldav.py
- tools/chemenu/tasks/config.py
- tools/chemenu/tasks/superproductivity.py
- tools/chemenu/telemetry/policy.py
- tools/chemenu/tests/test_config_shapes.py
- tools/chemenu/tests/test_doctor.py
- tools/chemenu/tests/test_reference_doc.py
- tools/chemenu/upload.py
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
Overlap only in kb/index.md, kb/log.md, kb/provenance.md and kb/**/INDEX.md no longer
fails a reconcile or reaches the rebase-review gate: the log keeps both sides' entries,
the catalog and provenance are regenerated. Uncommitted work no incoming commit touches
rides through the rebase via --autostash; the working tree is backed up under
refs/wikitool/reconcile-backup first. is_generated is narrowed to kb/.
Files changed:
- CHANGES.md
- VERSION
- instructions/gates.md
- instructions/session-setup.md
- tools/CONTRACT.md
- tools/chemenu/commands/git_publish.py
- tools/chemenu/commands/index_build.py
- tools/chemenu/commands/provenance_cmd.py
- tools/chemenu/tests/test_git_publish.py
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
The ON FAILURE reaction for an occupied folder name still said there is no
--replaces for a folder; for a captured bundle that sent a new edition down
the rename route. raw/CONTRACT.md names the manifest as a captured folder's
source of the capture fields.
Files changed:
- CHANGES.md
- VERSION
- raw/CONTRACT.md
- tools/CONTRACT.md
- tools/chemenu/commands/raw_cmd.py
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
New repo_capture module: resolve a branch or tag-pattern ref rule, fetch it
shallowly by name into a bare cache, read the glob-selected files as blobs,
and record repo/ref/commit/globs/capture fields in _capture.json. raw status
reports changed captured bundles as A/M/D; raw accept --replaces-bundle swaps
a captured bundle for its new edition at the same address. iter_raw_files now
skips _capture.json and anchors the CONTRACT.md exclusion to raw/CONTRACT.md.
Files changed:
- .gitignore
- CHANGES.md
- README.md
- VERSION
- instructions/wiki-ingest/SKILL.md
- raw/CONTRACT.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/dist_cmd.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/raw_cmd.py
- tools/chemenu/config.py
- tools/chemenu/repo_capture.py
- tools/chemenu/tests/test_cli.py
- tools/chemenu/tests/test_raw_capture.py
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
dist export leaves out tools/chemenu/tests/, tools/pytest.ini and tools/.coveragerc by exact
path - the suite tests the origin repository, and 257 of its tests failed in a fresh export.
dist upgrade now deletes a no-longer-shipped file that is unchanged since install, with any
directory that leaves empty, and blocks one changed since install like any local change
(--take-release deletes it, --keep-local keeps it). --prune is accepted and ignored.
Files changed:
- CHANGES.md
- EVALS.md
- VERSION
- instructions/mcp-read-server.md
- instructions/upgrade-instance.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/commands/dist_cmd.py
- tools/chemenu/tests/test_dist_cmd.py
- tools/chemenu/tests/test_dist_upgrade.py
- tools/requirements-mcp.txt
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
cli.py's typer._click.core.format_help patch was applied a second time
outside the try/except that exists to let a future typer without
typer._click degrade to plain Click help instead of crashing on import.
That second, unconditional line referenced two names the failed import
never defines, so the exact case the fallback exists for raised
NameError on every invocation instead. Removed; a subprocess test with
a targeted import hook (not sys.modules poisoning, which breaks typer
itself, and not importlib.reload, which would stay green against the
bug) pins that the fallback now actually falls back.
The new command's cli_contract record promised kb/concepts/<Name>.md
and kb/sources/Source - <Name>.md - both types have since grown a
layout: that files a page under a subtype-computed subdirectory, the
same rule an entity or a project already follows. Notes for concept
and source now name the subdirectory and where it comes from;
comparison was checked against its type-spec and left alone. Also
found and fixed: new source's example line omitted source_type,
fidelity and authority, so it could never succeed as written. A new
test reads each variant's note out of the record and checks the
written path against the pattern it promises, instead of against a
path re-typed into the test - which is what let the existing per-type
path tests stay green through this exact drift.
tools/CONTRACT.md regenerated via `wikitool docs contract --apply`;
pytest (1550), docs verify and instructions verify all green.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
torbenandClaude Opus 5.5