Run log — append-only¶

PHASE 0/1 — frame + evidence inventory¶

2026-07-26  FRAME       README.md, CLAUDE.md, docs/adr/*        → 00-frame.md written
2026-07-26  INVENTORY   evidence ranking below

Evidence available (ranked per extraction.md §1)¶

Consequence: the two highest-value evidence ranks (1, 5) are missing entirely. Every "frequency" and "actual impact" statement in 05-gaps.yaml is therefore unknown rather than measured. Recorded as issue-e183d47cdee1.

PHASE 2 — extraction¶

2026-07-26  P1 struct   entry_points/cli/app.py, dispatch.py      → 27 CLI commands, 18 wire commands
2026-07-26  P1 struct   alembic/versions/0001,0002                → 7 tables + 1 FTS5 virtual table
2026-07-26  P1 struct   documents/domain/{schema,entities,vo}     → Document aggregate, Schema, DocId, RelatedRef
2026-07-26  P1 struct   documents/infra/{profiles,default_schema} → core + 5 profiles, 12 types
2026-07-26  P2/P3       documents/application/services/*          → DocumentService, MaintenanceService call chains
2026-07-26  P2/P3       tags/application, indexing/*, agents/*    → per-module behaviour + ordering
2026-07-26  P2/P3       platform/{persistence,filesystem,transport}, entry_points/daemon
2026-07-26  P4/P5       all of the above                          → BR-001..BR-072 drafted
2026-07-26  READ        tests/** (28 files)                       → cross-check of P4; encoded intent
2026-07-26  SKIPPED     tach.toml, scripts/check_contract_sync.py → out of scope per 00-frame.md
2026-07-26  SKIPPED     assets/, docs/PUBLISHING.md, .github/     → out of scope per 00-frame.md
2026-07-26  SKIPPED     platform/persistence/alembic/env.py       → migration machinery, no business rule

Empirical probes (evidence rank 1-substitute: executed the real CLI)¶

Store fixtures under the session scratchpad; all runs --no-daemon, real SQLite, real files.

PROBE-1  clone->reindex->add    store1  → CONFIRMED id collision (GAP-003)
PROBE-2  get/query after PROBE-1 store1 → CONFIRMED first doc invisible to all read paths
PROBE-3  check --strict on 2 new docs   → exit 1 from `orphan` alone (GAP-006)
PROBE-4  context w/ resolved neighbour  → CONFIRMED inactive filter bypassed via graph (GAP-004)
PROBE-5  context --limit 3, 3x out-deg 2 → returned 9 docs (GAP-005)
PROBE-6  delete --force w/ incoming ref  → CONFIRMED dangling ref written to canonical file (GAP-007)
PROBE-7  update a doc holding dangling ref → CONFIRMED accepted, ref re-persisted (GAP-007)
PROBE-8  decision --related issue        → CONFIRMED permanent `layering` warning (GAP-008)
PROBE-9  delete then add                 → id NOT reused (counter monotonic) — no gap

2026-07-26  PROBE-10  6x concurrent --no-daemon add   → all returned adr-0002 (GAP-009)
2026-07-26  PROBE-11  same race WITH the daemon        → adr-0002..0007, unique — scopes GAP-009
2026-07-26  PROBE-12  schema validate on a typo'd transition target → {"valid":true} (GAP-010)
2026-07-26  PROBE-13  agent install --agent <typo>     → [], exit 0, no files (GAP-024)
2026-07-26  PROBE-14  context on unrelated query       → returns a doc, score 0.0328 (GAP-017)
2026-07-26  PROBE-15  all five profiles merged         → 15 types, no prefix collision — NO gap
2026-07-26  PROBE-16  delete then add                  → id not reused — NO gap

PHASE 3/4 — modeling + formalizing¶

2026-07-26  MODEL   01-actors.yaml     → 8 actors (2 of them absent-but-implied: ACT-007, ACT-008)
2026-07-26  MODEL   02-flows/          → 5 flows, 41 hotspots, 3 off-system step clusters
2026-07-26  MODEL   04-glossary.yaml   → 13 terms, 10 with recorded conflicts
2026-07-26  FORMAL  03-rules.yaml      → 45 rules (EARS), 3 decision tables, 5 marked `disputed`

PHASE 5 — gap detection¶

Coverage checklists from gap-checklists.md §2 iterated mechanically against every flow and the document / tag entities. Result: 39 gaps — 6 blocking, 20 material, 13 cosmetic.

Checklist items that produced findings: bulk import/export (issue-20933967697b), merge/deduplicate (issue-cc61d038cf8f), delete + compensating action (issue-fd547a293d01), every-state-has-an-exit (issue-b47a1203baa2), concurrent transition by two actors (issue-389dc5dac58a, issue-be95d3e242a3), duplicate submission / idempotency (issue-389dc5dac58a), admin override + audit (issue-0783d236d565), support diagnosis tooling (issue-476b4e188fab), notifications (issue-b4f441c7210f), time/timezone (issue-7e16dfe2521c), volume limits (issue-f6a5d0b86806), observability (issue-e183d47cdee1), migration of data created under older rules (issue-ed49c1d03894).

Checklist items examined and found adequately covered (recorded so coverage is not overstated): create validation (BR-001..BR-005), read visibility (BR-028, BR-029), field mutability by state (BR-005), transfer of ownership (--set-owner), retention (git holds history), permissions (N/A per adr-90e994d931cc), rounding/currency/tax (no money in this domain).

Smell scan (gap-checklists.md §3, automated regex over all 45 rule statements): 0 hits.

PHASE 7 — adversarial self-review¶

Ran against my own register, not the code. Four defects found and fixed:

SELF-1  GAP-013 was hedged ("advanced and committed... or not"). Re-read repositories.py —
        next_number only *flushes*, so the counter rolls back with the transaction while the
        already-written file survives. Rewritten as a concrete third duplicate-id path.
SELF-2  GAP-012 was severity:material but meets my own blocking rubric ("touches data loss").
        Raised to blocking; register re-sorted.
SELF-3  BR-034 has four conditions and no decision table — violates quality gate §9.
        Table added (verified against runner.py).
SELF-4  Q/BR/GAP cross-references were inconsistent after renumbering. Reconciled by script;
        verified no dangling or undefined ids in either direction.

Claims I attempted to refute and could not: issue-b7ddde3ce860, issue-8c37bf22ba3c, issue-996b567e5131, issue-9cb85759076d, issue-389dc5dac58a, issue-b47a1203baa2, issue-93152f7b9213, issue-b8220546282c — each is reproducible by the probe recorded above.

Claim I did refute and narrowed: an early reading that docir context --limit overflows in every case. PROBE-4 (--limit 1 → 1 result) shows it overflows only when selected documents have outgoing edges to documents not already selected. issue-996b567e5131 states that actual condition.

Quality gates (SKILL.md §9)¶

[x] Every actor appears in >=1 flow                     8/8
[x] Every flow has unwanted-behaviour rules per failure point
                                    BR-001..003, 010..012, 018, 043, 061, 064, 070, 071
[x] Every rule has an evidence pointer and a status     45/45 (verified by script)
[x] Every rule with >2 conditions has a decision table  BR-003, BR-005, BR-034
[x] Smell scan clean                                    0 hits across 45 statements
[x] Every glossary term has exactly one definition      13 terms; 10 conflicts recorded as gaps
[x] Every hotspot resolved into a rule/gap/assumption   41/41
[x] Coverage log lists what was not examined            below
[x] Adversarial pass run and findings addressed         4 found, 4 fixed

Coverage report — what was NOT examined¶

Not examined at all (out of scope per 00-frame.md, or no business rule inside): tach.toml, scripts/check_contract_sync.py, .github/workflows/, assets/, docs/PUBLISHING.md, pyproject.toml packaging metadata, platform/persistence/alembic/env.py, platform/embedding/fastembed.py (optional dependency, excluded from the project's own type-check and coverage).

Examined shallowly (read for structure, not line-by-line; rules here are lower-confidence): platform/transport/{protocol,client,messages}.py, entry_points/daemon/socket_executor.py, entry_points/cli/{body_input,rendering}.py beyond the trim logic, modules/agents/{domain,infra}/** beyond the service, modules/agents/infra/templates/skill.md.

Evidence classes entirely unavailable this run (see 00-frame.md): production behaviour, support tickets, logs, analytics, and any SME statement. Ranks 1, 5 and 6 of the evidence hierarchy are absent — which is why frequency is unknown on almost every gap and why every rule is status: assumed rather than confirmed.

Consequence for the reader: this register is a draft until the maintainer confirms it. An agent-produced rule register is not valid elicitation until the source agrees with it (questioning.md §5).

DELTA PASS — 2026-07-29, v0.7.0 (39 commits since the original run at 560aea5)¶

Scope: the surface added or changed since v0.2.1, not a re-derivation. The existing register was appended to, never rewritten (SKILL.md §1.6). 37 of 46 recorded gaps had been resolved; the question was what the fixing itself introduced.

FRAME    delta only: 34 source files changed, +1951/-265; 8 new CLI flags
INVENTORY same evidence ranks as the original run — 1, 5 and 6 still absent
EXTRACT  P1 via the Typer command tree (authoritative, not the docs)
DETECT   7 empirical probes against the real CLI, listed below

Probes¶

DELTA-PROBE-1  docir --home X init            → store created in CWD, X untouched   issue-638068ed09a6
DELTA-PROBE-2  init --force-schema (no --force) → silent no-op                      issue-9417ffd5306d
DELTA-PROBE-3  store field on read paths      → absent on query/search/context      issue-c2b4e38e76d9
DELTA-PROBE-4  query --stale --include-archived → correct; archived excluded by default — NO gap
DELTA-PROBE-5  check --fix with unknown-tag   → correctly returned in `remaining`  — NO gap
DELTA-PROBE-6  tag rename X X --merge         → registry entry deleted, docs keep the tag  issue-9bbca6c0f434
DELTA-PROBE-7  add --id in a random store     → adopted; next id still random      — NO gap

Three of seven probes found nothing. Recorded so the coverage is not overstated: the stale/archived interaction, check --fix's handling of the new finding kinds, and cross-style id adoption are all correct.

What the delta pass was for¶

Two of the four findings were introduced by the fixes themselves, which is the argument for running one at all:

• GAP-048 (self-merge corrupts the registry) came from the GAP-028 merge, four commits earlier. Its tests asked "does merging two tags work?" and never "what if they are the same tag?". It shipped in 0.7.0 and manufactured precisely the unknown-tag state that the GAP-016 work had taught check to detect — one fix creating the condition another fix had just learned to report.
• GAP-050 came from the GAP-023 fix, which reasoned about writes and did not ask whether reads have the same question. GAP-049 came from the GAP-026 fix.

A feature added to close a gap is new surface, and its degenerate cases are unexamined by construction — the tests written alongside it are shaped by the gap it was closing.

GAP-047 is different: it predates the original run and that run missed it. init is the one command that builds its own home rather than using the resolved settings, so it fell outside a review that traced Settings.resolve. Worth remembering that "every command does X" is a claim to verify per command, not per resolver.

Coverage — what this pass did NOT examine¶

Unchanged since v0.2.1 and not re-read: the daemon transport and lifecycle, the embedding scheduler, lint --deep, the agents module beyond the template, and Alembic. The nine cosmetic gaps left open from the original run were not re-examined either; they were assessed for priority on 2026-07-29 (see the entries) but not re-derived from code.

About the analysis/ paths in this log¶

This document was analysis/99-log.md until the discovery bundle was folded into docir's own store. The analysis/... paths in the text above describe where the run wrote its output at the time; those files are documents in this store now — see docs/README.md for the map. The gap issues that cite this log link to it as a typed edge.