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kb init: register each page once in a new repository index - #261

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kb/init-index-single-registration
Sep 30, 2026
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kb/init-index-single-registration

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@tzhouam tzhouam commented Sep 30, 2026

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Summary

The jiuwenswarm pilot (empty knowledge base, skeleton, dry run) blocked after all its model calls: the generated index intro linked architecture.md and the deterministic contents list linked it again, and check_knowledge_tree.py refuses a page registered twice in its directory index (页面在当前目录索引中重复登记).

In a new index the contents list is now each page's only registration:

  • init_stages.unlink_listed turns intro links to listed pages into their labels (angle destinations and titles handled; anchors and ./ ignored; images and other targets untouched).
  • The result is re-checked with the same CommonMark parser L1 uses (new public knowledge_service.l1.link_targets). If a link to a listed page survives in a form the rewrite does not know (e.g. a reference link), the optional intro is dropped and a checklist note is added — a page is never registered twice.

Tests

test_kb_init_skeleton.py: unlink unit tests (plain, angle, titles, anchors, images, other targets), the pilot regression end to end, angle-link intro, reference-link intro dropped with a checklist note. Commit gate approved (round 2 after an angle-link finding); local CI mirror green.

Stacked on #259.

🤖 Generated with Claude Code

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💡 Codex Review

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Reviewed commit: d8a3059285

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at = lines.index(intro)
lines[at] = unlink_listed(intro, listed)
resolved = {posixpath.normpath(posixpath.join(directory, link)) for link in listed}
if link_targets(directory, lines[at]) & resolved:

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P2 Badge Account for images in the duplicate-registration check

When a generated intro contains an image whose destination is a listed page, such as ![architecture](architecture.md), unlink_listed deliberately leaves it unchanged and this CommonMark-based check sees no surviving link because l1._links excludes images. However, the mandatory knowledge/tools/check_knowledge_tree.py validator extracts images with MARKDOWN_LINK and counts that destination as a registration, so the image plus the generated contents entry still produces “页面在当前目录索引中重复登记” and blocks the skeleton stage. The fallback must use the validator's registration semantics (or remove matching image destinations) rather than only link_targets.

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tzhouam and others added 8 commits September 30, 2026 23:36
Stage 1 of kb init (design kb-init v3): bootstrap a repository's
knowledge base from its docs and seed pages, as one human-merged PR.

- init_budget: hard per-stage ceiling by reservation. A generator call
  reserves threshold + one worst-case request (claude's
  --max-budget-usd only stops the next request); models without a price
  are refused before any call. Judge calls are accounted at a fixed cost.
- init_support: InitRuntime (never KbRuntime, so never kb.db), the
  per-stage InitRecord, the upstream pin (bare mirror; the pin defaults
  to the mirror's HEAD, i.e. the upstream default branch, never an
  assumed main; safe export; PinnedObserver), model calls through the
  budget, claim/evidence and outside-knowledge path checks, the CI
  knowledge validators on the result, and InitPublisher (one
  deterministic commit on an exact base, pushed to a branch that must
  not exist, PR via the owner's gh; or a local dry run). Writes need
  ALLOW_PUSH=1, ALLOW_POST=1 and KB_INIT_GIT_AUTHOR (checked before any
  model call); private upstreams are always dry runs. INIT_PATHS allows
  knowledge/repos/_index.md, the shared list a new repository joins.
- init_stages: run_stage + validate_change (the only
  check_changeset(bootstrap=True) caller). Skeleton: map call (entry
  page, architecture page, routes, general links), doc-invariant rules,
  adapted seed pages. Every rule is D5-filtered, evidenced and checked at
  the pin, then PLACED on a running tree before judging (a page that
  fills up sends the rule to a sibling page), so the advisory judge sees
  each rule where it is written; fail verdicts are stripped. Existing
  pages are only appended to; routes start from owners read
  deterministically from existing sub-directory entry pages (code paths
  they name that exist at the pin); findings on existing pages go to the
  PR checklist; a failed push is recorded as blocked. suggest_seeds
  ranks candidates without a model call.
- InitConfig gains generator_call_usd and harness_overhead_bytes;
  build_doc_corpus takes optional globs (doc_files).
- knowledge.init step, kb-init playbook, `kb init REPO --stage S
  [--dry-run] [--pin SHA]` and `kb init REPO --suggest-seeds`, dispatched
  before any ledger is opened.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
L1 reads any line starting with "## <Word>" as a rule ID
(lifecycle.RULE_HEADING / ANY_RULE_HEADING), so a model-written
"## Overview" or "## SERV-1 — x" in architecture.md or the entry page
intro could collide with real rule IDs or masquerade as a rule. Every
non-rule page the skeleton writes now goes through neutral_headings: an
ATX heading outside code becomes a bold paragraph, any other line that
starts with "#" is escaped, and such a line inside a fence is indented
by one space. No line starts with "#", so the rule regexes (all anchored
at column 0) can never match. The entry page's list heading is bold too.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Stage 2 of kb init (design v3 §7.1-7.2): route every code module.

- init_stages: the skeleton's flow becomes a _Stage base shared by every
  stage (pin, record, rule screening and placement, the deterministic
  checks as _conclude, the publication); _Skeleton keeps only its own
  steps. New: the stage chain. Each earlier stage must be merged (record
  published and gh pr view MERGED, so main holds it), or, for a dry run
  of this stage, dry-run: its snapshot is overlaid on main as the base and
  handed to the knowledge validators with this stage's change. A stage
  with nothing to change is recorded "empty", not blocked. Later stages
  keep the earlier stages' pin unless --pin says otherwise.
- init_modules: scan_modules_at_depth at the pin (language from the
  adapter's repo.language; none or unknown -> no scan, checklist). A
  module an owner partly reaches is absorbed: its prefix is appended to
  that owner's scope_prefixes. Every other module gets one bounded
  generator call (file names, signatures, leading docstrings, never
  bodies) and a map card: a prose page (type architecture) in an existing
  components/<group>/ (index append-only) or a new group with its own
  _index.md and route owner, linked upward. Sections are bold labels: the
  knowledge format reads any "## <Word>" heading as a rule ID. The route
  table is only appended to (routes_append_only). Budget or card cap ->
  the cards written so far still make a PR; the rest is listed.
- InitRecord.coverage: the stage's coverage report, rendered as a
  before/after table in the PR body.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Stage 3 of kb init (design v3 §7.3, §9 PR 3).

- UpstreamPin.first_parent_changes: the PR window, read offline from the
  mirror: the files each of the last pr_window_count first-parent commits
  up to the pin changed, no older than pr_window_max_age_days before the
  PIN's commit time (a function of the pin, never of the clock).
- init_deepen: modules by churn in the window, highest first. A module no
  route reaches, or whose owner already bears rules (the page itself, or a
  page in the same directory, has an active rule), is skipped. Every other
  module gets one generator call that reads its code at the pin (numbered,
  byte-bounded) and proposes rules with line-ranged evidence, which must lie
  inside the module. They go through the shared screening (D5, pinned
  evidence and claims, placement, advisory judge) and are appended to the
  owner's rule page, or rules.md beside it; existing rules are never
  edited. Stops at coverage_target (rule-bearing PR-weighted), when the
  budget runs out, or at the end of the list. The record reports routed
  and rule-bearing coverage before/after and the hot paths still without
  rules.
- The shadow flip in the same PR: flip_to_shadow edits exactly the
  enabled / mode lines of the adapter's knowledge_lifecycle block
  (inserting enabled under the header if missing); comments and every
  other line are kept. _check_flip accepts only that manifest,
  check_flip_to_shadow, and parse_lifecycle on the head (on, shadow, same
  knowledge dir). A manifest without the block blocks before any model
  call.
- init_modules.scan_modules is now a module function both stages use.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The last kb init stage (design v3 §11). After the deepen PR merged (a dry
run chains on the dry-run snapshots), it compares what the advisory judge
said about every rule init wrote with what the owner merged, and proposes
adapters/<adapter>/kb-calibration/cases/*.json plus
knowledge_lifecycle.calibration_set: kb-calibration as its own PR.

- Stage records now keep the judged rule text and its pinned evidence in
  each verdict, so rules the judge stripped or the owner deleted can be
  turned into cases.
- Labels follow the design table: kept pass/unsure/unjudged -> good
  (source owner); stripped fail -> bad (source judge); deleted or
  rewritten pass -> bad with override; deleted or rewritten
  unsure/unjudged -> bad (source owner). A rewritten rule's case holds
  the text the judge saw.
- Cases are self-contained in the load_cases shape: the page without the
  rule as base, the judged text re-applied through apply_operations as
  head, evidence re-read from the pinned mirror. A case that does not pass
  L1 on its own is left out and noted. Case IDs carry the stage: an ID
  one stage's judge stripped can be reassigned by a later stage.
- Deterministic mutations of good rules (broken path claim, shifted
  evidence range, negated invariant, a sibling module's evidence) balance
  the set and top owner-sourced bad cases up to five (a broken path must
  really be absent at the pin, a moved range must show different text);
  with fewer than five bad cases from the owner or from mutations the
  stage is blocked, since the judge's own fails cannot calibrate it; so
  it is with no good case at all (kb calibrate never passes without one).
- The manifest edit is one line (set_calibration_set), checked with
  check_lifecycle_flip(allowed=CALIBRATION_KEYS) and parse_lifecycle;
  existing cases are never overwritten.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Found by the first afd-plugin pilot (skeleton, dry run):

- The adapter's repos/ seed was a type: guide page; the skeleton only
  adapted type: rule pages, so it was skipped with no trace, which the
  design forbids (a seed is never skipped silently). Any content page a
  seed names is now adapted (indexes are navigation, not content). A
  seed naming no content page goes on the checklist, a page that
  transfers no rule goes in the notes, and a budget stop lists that
  seed and every one after it as unfinished.
- The PR body said "Model spend (accounted): $0.00" while the record
  held $7.42: spent_usd was written in the stage's finally block, after
  the body was rendered. It is now written before rendering.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…dule with an ancestor prefix

The afd-plugin pilot (dry run) made the coverage metric meaningless. The
skeleton wrote an aggregate owner "components" listing its components'
prefixes; the modules stage absorbed the package root by appending
afd_plugin/ to it, a catch-all that matches every file; deepen gave the
hottest module to that owner (it reached as many files as the component
owner and came first in routing order) and wrote 12 rules to
components/rules.md; and pr_weighted_coverage counted a file rule-bearing
when ANY matching owner had rules, so coverage jumped 10% -> 100% and
deepen stopped with 8 hot modules untouched.

- init_coverage.most_specific: the owners with the longest matching
  prefix, then the deepest page (a component's own page beats an
  aggregate entry page listing the same area); rule-bearing now uses
  only those. shadowing() lists directory prefixes that are strict
  ancestors of another owner's prefix.
- init_modules: absorption picks the owner that owns most of the
  module's files most specifically, and cover_prefixes adds only
  prefixes for the module's own unrouted files: the module directory
  when no other module or OTHER owner's prefix lies under it, else the
  highest such directory per file, else the file. A module needing more
  than 20 prefixes gets a map card instead; card owners use the same
  cover.
- init_deepen: a module's owner is its most specific owner; "already
  bears rules" and the uncovered-hot list use the same rule.
- skeleton: a checklist note names every owner prefix that shadows
  other owners' prefixes, so the owner can narrow it.

Replayed offline on the pilot's pin: the root absorbs 4 files instead of
afd_plugin/, the hottest module goes to execution-platforms, and rules
on the aggregate page now count for 4.5%, not 100%.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…pped

The afd-plugin pilot re-run on #258 wrote 36 rules on 3 owner pages,
reached 74% rule-bearing coverage of an 85% target, and stopped with no
note and nothing unfinished. The hottest files still without rules
(v1/worker/attention_model_runner.py, ffn_model_runner.py, ...) sit in
modules already visited, but their most specific owners (attention-runtime,
ffn-runtime) differ from the module's majority owner, and the loop went
module by module, so it never reached them.

- Deepen now works on groups: the files of one module that share one most
  specific owner. Groups are ordered by churn; one bounded generator call
  per group sees only that group's files, and evidence must lie in them.
  A group whose owner already bears rules is skipped (counted). Caps,
  budget reservation, D5, pinned claims and the advisory judge are
  unchanged.
- The stop reason is always recorded in the notes (and so the PR body):
  target reached, budget exhausted (the remaining groups stay in
  unfinished, labelled with their owner), or "every hot group visited;
  target not reached (X% < Y%)" with the five hottest files still without
  rules. Hot files no route reaches are listed too. The pass never ends
  below target silently.

Replayed offline on the pilot (no model calls): from the pre-deepen state
the loop makes 5 calls (execution-platforms, model-integration,
connectors, attention-runtime, ffn-runtime) and reaches 81.8%; after the
module-loop re-run, exactly the attention-runtime and ffn-runtime groups
remain to visit.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@tzhouam
tzhouam force-pushed the kb/init-deepen-by-owner branch from d423c09 to 45feb0e Compare September 30, 2026 15:37
The jiuwenswarm pilot (empty knowledge base, skeleton, dry run) blocked
after all model calls: the generated index intro linked architecture.md
and the deterministic contents list linked it again, and the
knowledge-tree validator refuses a page registered twice in its
directory index. In a new index the contents list is now each page's
only registration: intro links to listed pages become their labels
(angle destinations and titles handled; anchors and ./ ignored; images
and other targets untouched). The result is then checked with the same
CommonMark parser L1 uses (new public l1.link_targets): if a link to a
listed page survives in a form the rewrite does not know (e.g. a
reference link), the optional intro is dropped and a checklist note is
added, so a page is never registered twice.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@tzhouam
tzhouam force-pushed the kb/init-index-single-registration branch from d8a3059 to b39d50a Compare September 30, 2026 15:38
@tzhouam
tzhouam changed the base branch from kb/init-deepen-by-owner to main September 30, 2026 15:38
@tzhouam
tzhouam merged commit 87e74fb into main Sep 30, 2026
2 checks passed
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