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1a408b3
fix: critical performance improvements from production feedback
tom-dyar Oct 15, 2025
911cb05
chore: sync from internal repository (2025-10-16)
tom-dyar Oct 16, 2025
2e462e9
feat: complete production-grade REST API implementation (T001-T058)
tom-dyar Oct 17, 2025
b715805
chore: sync from internal repository (2025-10-17)
tom-dyar Oct 17, 2025
60512b0
feat: add MCP tools, pipeline validation, and multi-query RRF
tom-dyar Oct 22, 2025
e153c65
docs: update changelog [skip ci]
actions-user Oct 22, 2025
683c314
docs: rewrite README with developer focus and accurate pipeline info
tom-dyar Oct 22, 2025
8d5f1ea
fix(graphrag): fix 3 critical entity extraction bugs blocking production
tom-dyar Oct 22, 2025
ef909ca
docs: update changelog [skip ci]
actions-user Oct 22, 2025
0d0a6a7
fix(graphrag): fix Bug #5 - GPT-OSS individual extraction and API key…
tom-dyar Oct 22, 2025
8811987
fix(graphrag): fix Bug #6 - LiteLLM model name prefix stripping
tom-dyar Oct 22, 2025
5d41853
docs: update changelog [skip ci]
actions-user Oct 22, 2025
52ddfe8
fix(graphrag): replace register_custom_models with DirectOpenAILM for…
tom-dyar Oct 22, 2025
534475a
chore: update redaction log from sync
tom-dyar Oct 22, 2025
c81a854
fix(graphrag): fix false negative entity extraction validation bug
tom-dyar Oct 30, 2025
4cf7823
fix(graphrag): complete fix for entity extraction validation bug
tom-dyar Oct 30, 2025
cbbcf3b
feat(embeddings): add module-level cache for SentenceTransformer models
tom-dyar Nov 5, 2025
3fba1e3
docs: update changelog [skip ci]
actions-user Nov 5, 2025
1aaefc6
fix: resolve PyPI build error and bump to v0.2.1
tom-dyar Nov 6, 2025
029ba01
chore: update package description and bump to v0.2.2
tom-dyar Nov 6, 2025
8088866
fix: include all subpackages in distribution (v0.2.3)
tom-dyar Nov 6, 2025
126b057
chore: sync from internal repository after PyPI packaging updates
tom-dyar Nov 6, 2025
c88b08f
docs: update changelog [skip ci]
actions-user Nov 6, 2025
648e5c9
chore: sync redaction changes from internal repository
tom-dyar Nov 6, 2025
4119f35
chore: sync from internal repository (2025-11-08)
tom-dyar Nov 8, 2025
b2c9efa
docs: update changelog [skip ci]
actions-user Nov 8, 2025
e0aee07
gitignore tracking files
tom-dyar Nov 8, 2025
89dd18f
fix: eliminate 99.96% redundant table existence checks in EntityStora…
tom-dyar Nov 8, 2025
f8b85b6
chore: migrate specs and constitution from ../rag-templates
tom-dyar Nov 8, 2025
26590c7
fix: resolve 4 bugs in Feature 051 IRIS EMBEDDING implementation
tom-dyar Nov 8, 2025
1ca30d5
fix: replace datetime.UTC with timezone.utc for Python compatibility
tom-dyar Nov 8, 2025
abd582a
docs: add Feature 051 completion summary
tom-dyar Nov 8, 2025
2283e0f
chore: add fork workflow documentation and update constitution
tom-dyar Nov 8, 2025
516db67
docs: update constitution with fork-based workflow (v1.8.0)
tom-dyar Nov 8, 2025
08986d8
chore: bump version to 0.3.0 for PyPI release
tom-dyar Nov 9, 2025
982cfe7
fix: EntityExtractionService now respects root-level LLM config (v0.3.1)
tom-dyar Nov 9, 2025
138de63
fix: add comprehensive logging for entity extraction (v0.3.2)
tom-dyar Nov 9, 2025
5c2a804
fix: add comprehensive entity extraction logging to EntityExtractionS…
tom-dyar Nov 9, 2025
9bcfb6d
BREAKING CHANGE: rename module iris_rag to iris_vector_rag (v0.4.1)
tom-dyar Nov 9, 2025
095d3ce
fix: move common module inside iris_vector_rag to resolve namespace c…
tom-dyar Nov 9, 2025
eb575ed
fix: rebuild package correctly with proper structure (v0.5.1)
tom-dyar Nov 9, 2025
223e53f
docs: update constitution with critical PyPI publishing procedures (v…
tom-dyar Nov 9, 2025
7c4ecf6
docs: Feature 055 - comprehensive documentation review and README opt…
tom-dyar Nov 10, 2025
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101 changes: 101 additions & 0 deletions .claude/commands/analyze.md
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---
description: Perform a non-destructive cross-artifact consistency and quality analysis across spec.md, plan.md, and tasks.md after task generation.
---

The user input to you can be provided directly by the agent or as a command argument - you **MUST** consider it before proceeding with the prompt (if not empty).

User input:

$ARGUMENTS

Goal: Identify inconsistencies, duplications, ambiguities, and underspecified items across the three core artifacts (`spec.md`, `plan.md`, `tasks.md`) before implementation. This command MUST run only after `/tasks` has successfully produced a complete `tasks.md`.

STRICTLY READ-ONLY: Do **not** modify any files. Output a structured analysis report. Offer an optional remediation plan (user must explicitly approve before any follow-up editing commands would be invoked manually).

Constitution Authority: The project constitution (`.specify/memory/constitution.md`) is **non-negotiable** within this analysis scope. Constitution conflicts are automatically CRITICAL and require adjustment of the spec, plan, or tasks—not dilution, reinterpretation, or silent ignoring of the principle. If a principle itself needs to change, that must occur in a separate, explicit constitution update outside `/analyze`.

Execution steps:

1. Run `.specify/scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks` once from repo root and parse JSON for FEATURE_DIR and AVAILABLE_DOCS. Derive absolute paths:
- SPEC = FEATURE_DIR/spec.md
- PLAN = FEATURE_DIR/plan.md
- TASKS = FEATURE_DIR/tasks.md
Abort with an error message if any required file is missing (instruct the user to run missing prerequisite command).

2. Load artifacts:
- Parse spec.md sections: Overview/Context, Functional Requirements, Non-Functional Requirements, User Stories, Edge Cases (if present).
- Parse plan.md: Architecture/stack choices, Data Model references, Phases, Technical constraints.
- Parse tasks.md: Task IDs, descriptions, phase grouping, parallel markers [P], referenced file paths.
- Load constitution `.specify/memory/constitution.md` for principle validation.

3. Build internal semantic models:
- Requirements inventory: Each functional + non-functional requirement with a stable key (derive slug based on imperative phrase; e.g., "User can upload file" -> `user-can-upload-file`).
- User story/action inventory.
- Task coverage mapping: Map each task to one or more requirements or stories (inference by keyword / explicit reference patterns like IDs or key phrases).
- Constitution rule set: Extract principle names and any MUST/SHOULD normative statements.

4. Detection passes:
A. Duplication detection:
- Identify near-duplicate requirements. Mark lower-quality phrasing for consolidation.
B. Ambiguity detection:
- Flag vague adjectives (fast, scalable, secure, intuitive, robust) lacking measurable criteria.
- Flag unresolved placeholders (TODO, TKTK, ???, <placeholder>, etc.).
C. Underspecification:
- Requirements with verbs but missing object or measurable outcome.
- User stories missing acceptance criteria alignment.
- Tasks referencing files or components not defined in spec/plan.
D. Constitution alignment:
- Any requirement or plan element conflicting with a MUST principle.
- Missing mandated sections or quality gates from constitution.
E. Coverage gaps:
- Requirements with zero associated tasks.
- Tasks with no mapped requirement/story.
- Non-functional requirements not reflected in tasks (e.g., performance, security).
F. Inconsistency:
- Terminology drift (same concept named differently across files).
- Data entities referenced in plan but absent in spec (or vice versa).
- Task ordering contradictions (e.g., integration tasks before foundational setup tasks without dependency note).
- Conflicting requirements (e.g., one requires to use Next.js while other says to use Vue as the framework).

5. Severity assignment heuristic:
- CRITICAL: Violates constitution MUST, missing core spec artifact, or requirement with zero coverage that blocks baseline functionality.
- HIGH: Duplicate or conflicting requirement, ambiguous security/performance attribute, untestable acceptance criterion.
- MEDIUM: Terminology drift, missing non-functional task coverage, underspecified edge case.
- LOW: Style/wording improvements, minor redundancy not affecting execution order.

6. Produce a Markdown report (no file writes) with sections:

### Specification Analysis Report
| ID | Category | Severity | Location(s) | Summary | Recommendation |
|----|----------|----------|-------------|---------|----------------|
| A1 | Duplication | HIGH | spec.md:L120-134 | Two similar requirements ... | Merge phrasing; keep clearer version |
(Add one row per finding; generate stable IDs prefixed by category initial.)

Additional subsections:
- Coverage Summary Table:
| Requirement Key | Has Task? | Task IDs | Notes |
- Constitution Alignment Issues (if any)
- Unmapped Tasks (if any)
- Metrics:
* Total Requirements
* Total Tasks
* Coverage % (requirements with >=1 task)
* Ambiguity Count
* Duplication Count
* Critical Issues Count

7. At end of report, output a concise Next Actions block:
- If CRITICAL issues exist: Recommend resolving before `/implement`.
- If only LOW/MEDIUM: User may proceed, but provide improvement suggestions.
- Provide explicit command suggestions: e.g., "Run /specify with refinement", "Run /plan to adjust architecture", "Manually edit tasks.md to add coverage for 'performance-metrics'".

8. Ask the user: "Would you like me to suggest concrete remediation edits for the top N issues?" (Do NOT apply them automatically.)

Behavior rules:
- NEVER modify files.
- NEVER hallucinate missing sections—if absent, report them.
- KEEP findings deterministic: if rerun without changes, produce consistent IDs and counts.
- LIMIT total findings in the main table to 50; aggregate remainder in a summarized overflow note.
- If zero issues found, emit a success report with coverage statistics and proceed recommendation.

Context: $ARGUMENTS
158 changes: 158 additions & 0 deletions .claude/commands/clarify.md
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---
description: Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
---

The user input to you can be provided directly by the agent or as a command argument - you **MUST** consider it before proceeding with the prompt (if not empty).

User input:

$ARGUMENTS

Goal: Detect and reduce ambiguity or missing decision points in the active feature specification and record the clarifications directly in the spec file.

Note: This clarification workflow is expected to run (and be completed) BEFORE invoking `/plan`. If the user explicitly states they are skipping clarification (e.g., exploratory spike), you may proceed, but must warn that downstream rework risk increases.

Execution steps:

1. Run `.specify/scripts/bash/check-prerequisites.sh --json --paths-only` from repo root **once** (combined `--json --paths-only` mode / `-Json -PathsOnly`). Parse minimal JSON payload fields:
- `FEATURE_DIR`
- `FEATURE_SPEC`
- (Optionally capture `IMPL_PLAN`, `TASKS` for future chained flows.)
- If JSON parsing fails, abort and instruct user to re-run `/specify` or verify feature branch environment.

2. Load the current spec file. Perform a structured ambiguity & coverage scan using this taxonomy. For each category, mark status: Clear / Partial / Missing. Produce an internal coverage map used for prioritization (do not output raw map unless no questions will be asked).

Functional Scope & Behavior:
- Core user goals & success criteria
- Explicit out-of-scope declarations
- User roles / personas differentiation

Domain & Data Model:
- Entities, attributes, relationships
- Identity & uniqueness rules
- Lifecycle/state transitions
- Data volume / scale assumptions

Interaction & UX Flow:
- Critical user journeys / sequences
- Error/empty/loading states
- Accessibility or localization notes

Non-Functional Quality Attributes:
- Performance (latency, throughput targets)
- Scalability (horizontal/vertical, limits)
- Reliability & availability (uptime, recovery expectations)
- Observability (logging, metrics, tracing signals)
- Security & privacy (authN/Z, data protection, threat assumptions)
- Compliance / regulatory constraints (if any)

Integration & External Dependencies:
- External services/APIs and failure modes
- Data import/export formats
- Protocol/versioning assumptions

Edge Cases & Failure Handling:
- Negative scenarios
- Rate limiting / throttling
- Conflict resolution (e.g., concurrent edits)

Constraints & Tradeoffs:
- Technical constraints (language, storage, hosting)
- Explicit tradeoffs or rejected alternatives

Terminology & Consistency:
- Canonical glossary terms
- Avoided synonyms / deprecated terms

Completion Signals:
- Acceptance criteria testability
- Measurable Definition of Done style indicators

Misc / Placeholders:
- TODO markers / unresolved decisions
- Ambiguous adjectives ("robust", "intuitive") lacking quantification

For each category with Partial or Missing status, add a candidate question opportunity unless:
- Clarification would not materially change implementation or validation strategy
- Information is better deferred to planning phase (note internally)

3. Generate (internally) a prioritized queue of candidate clarification questions (maximum 5). Do NOT output them all at once. Apply these constraints:
- Maximum of 5 total questions across the whole session.
- Each question must be answerable with EITHER:
* A short multiple‑choice selection (2–5 distinct, mutually exclusive options), OR
* A one-word / short‑phrase answer (explicitly constrain: "Answer in <=5 words").
- Only include questions whose answers materially impact architecture, data modeling, task decomposition, test design, UX behavior, operational readiness, or compliance validation.
- Ensure category coverage balance: attempt to cover the highest impact unresolved categories first; avoid asking two low-impact questions when a single high-impact area (e.g., security posture) is unresolved.
- Exclude questions already answered, trivial stylistic preferences, or plan-level execution details (unless blocking correctness).
- Favor clarifications that reduce downstream rework risk or prevent misaligned acceptance tests.
- If more than 5 categories remain unresolved, select the top 5 by (Impact * Uncertainty) heuristic.

4. Sequential questioning loop (interactive):
- Present EXACTLY ONE question at a time.
- For multiple‑choice questions render options as a Markdown table:

| Option | Description |
|--------|-------------|
| A | <Option A description> |
| B | <Option B description> |
| C | <Option C description> | (add D/E as needed up to 5)
| Short | Provide a different short answer (<=5 words) | (Include only if free-form alternative is appropriate)

- For short‑answer style (no meaningful discrete options), output a single line after the question: `Format: Short answer (<=5 words)`.
- After the user answers:
* Validate the answer maps to one option or fits the <=5 word constraint.
* If ambiguous, ask for a quick disambiguation (count still belongs to same question; do not advance).
* Once satisfactory, record it in working memory (do not yet write to disk) and move to the next queued question.
- Stop asking further questions when:
* All critical ambiguities resolved early (remaining queued items become unnecessary), OR
* User signals completion ("done", "good", "no more"), OR
* You reach 5 asked questions.
- Never reveal future queued questions in advance.
- If no valid questions exist at start, immediately report no critical ambiguities.

5. Integration after EACH accepted answer (incremental update approach):
- Maintain in-memory representation of the spec (loaded once at start) plus the raw file contents.
- For the first integrated answer in this session:
* Ensure a `## Clarifications` section exists (create it just after the highest-level contextual/overview section per the spec template if missing).
* Under it, create (if not present) a `### Session YYYY-MM-DD` subheading for today.
- Append a bullet line immediately after acceptance: `- Q: <question> → A: <final answer>`.
- Then immediately apply the clarification to the most appropriate section(s):
* Functional ambiguity → Update or add a bullet in Functional Requirements.
* User interaction / actor distinction → Update User Stories or Actors subsection (if present) with clarified role, constraint, or scenario.
* Data shape / entities → Update Data Model (add fields, types, relationships) preserving ordering; note added constraints succinctly.
* Non-functional constraint → Add/modify measurable criteria in Non-Functional / Quality Attributes section (convert vague adjective to metric or explicit target).
* Edge case / negative flow → Add a new bullet under Edge Cases / Error Handling (or create such subsection if template provides placeholder for it).
* Terminology conflict → Normalize term across spec; retain original only if necessary by adding `(formerly referred to as "X")` once.
- If the clarification invalidates an earlier ambiguous statement, replace that statement instead of duplicating; leave no obsolete contradictory text.
- Save the spec file AFTER each integration to minimize risk of context loss (atomic overwrite).
- Preserve formatting: do not reorder unrelated sections; keep heading hierarchy intact.
- Keep each inserted clarification minimal and testable (avoid narrative drift).

6. Validation (performed after EACH write plus final pass):
- Clarifications session contains exactly one bullet per accepted answer (no duplicates).
- Total asked (accepted) questions ≤ 5.
- Updated sections contain no lingering vague placeholders the new answer was meant to resolve.
- No contradictory earlier statement remains (scan for now-invalid alternative choices removed).
- Markdown structure valid; only allowed new headings: `## Clarifications`, `### Session YYYY-MM-DD`.
- Terminology consistency: same canonical term used across all updated sections.

7. Write the updated spec back to `FEATURE_SPEC`.

8. Report completion (after questioning loop ends or early termination):
- Number of questions asked & answered.
- Path to updated spec.
- Sections touched (list names).
- Coverage summary table listing each taxonomy category with Status: Resolved (was Partial/Missing and addressed), Deferred (exceeds question quota or better suited for planning), Clear (already sufficient), Outstanding (still Partial/Missing but low impact).
- If any Outstanding or Deferred remain, recommend whether to proceed to `/plan` or run `/clarify` again later post-plan.
- Suggested next command.

Behavior rules:
- If no meaningful ambiguities found (or all potential questions would be low-impact), respond: "No critical ambiguities detected worth formal clarification." and suggest proceeding.
- If spec file missing, instruct user to run `/specify` first (do not create a new spec here).
- Never exceed 5 total asked questions (clarification retries for a single question do not count as new questions).
- Avoid speculative tech stack questions unless the absence blocks functional clarity.
- Respect user early termination signals ("stop", "done", "proceed").
- If no questions asked due to full coverage, output a compact coverage summary (all categories Clear) then suggest advancing.
- If quota reached with unresolved high-impact categories remaining, explicitly flag them under Deferred with rationale.

Context for prioritization: $ARGUMENTS
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