refactor: resolve all 44 audit findings across sigint plugin

[zircote]

Summary

• Resolve all 44 findings from comprehensive sigint plugin audit across architecture, security, prompt/skill, and code quality domains
• Security posture improved from 4/10 → 7/10
• Eval coverage expanded from 252 → 271 cases (3 new skill eval files)

Changes

Security (7 findings)

• SEC-01: Hardened dependabot-automerge.yml — actor guard (dependabot[bot]) + SHA pinning
• SEC-02: <untrusted_data> XML delimiters at all 4 codex review gates
• SEC-03: <user_input> tags + input sanitization (200-char truncation, backtick/angle-bracket stripping) in all 5 orchestration skills
• SEC-04/07: Threat model + in-scope categories + Security Advisories link in SECURITY.md
• SEC-05: apply_command_note: "MANUAL ONLY" guard in repo-metadata.json
• SEC-06: .env, *.env, *.bak added to .gitignore

Architecture (16 findings)

• ARCH-01/02: Fixed tool permissions in 2 agents + 3 commands
• ARCH-03: Standardized 85+ {topic-slug} → {topic_slug} across all source files
• ARCH-05: Fixed 5× codex:codex-rescue → codex:rescue
• ARCH-04/06/07/08/09/10/11: Blackboard resilience, team name fix, duplicate derivation, allowed-tools, error handling, return path
• ARCH-12–16: Step renumbering, heading dedup, Mermaid tools, field name, ID stability docs

Prompt/Skill Architecture (11 findings)

• PROMPT-01: New protocols/TREND-INDICATORS.md — shared INC/DEC/CONST definitions referenced by 8 skills
• PROMPT-02: Universal confidence scale (High/Medium/Low) in all 8 methodology skills
• PROMPT-03–07: Mermaid xychart-beta fix, placeholder contradictions, customer-research output rules, regulatory disclaimer
• PROMPT-08–11: Slug-format skill names, date placeholder instruction, interview timing note, conditional diagrams

Code Quality (10 findings)

• QUAL-01: New eval files for augment (4 cases), report (3 cases), migrate (3 cases)
• QUAL-02: Converted 8 output_matches → regex_match across 4 eval files
• QUAL-03/04: Strengthened config cascade + conflict detection evals with fixture data
• QUAL-05–10: Config fix, .bak protection, polling pattern, chunk limits, dry-run fallback, naming docs

Quality Scores

Metric	Score
Clean Code	8/10
Architecture	8/10
Security Posture	7/10 (was 4/10)

Test Plan

• All 271 eval cases verified (252 baseline + 19 new)
• Zero output_matches remaining (all converted to regex_match)
• Zero {topic-slug} remaining in source files
• Zero codex:codex-rescue remaining
• 3 evaluator passes (1 per iteration) — all PASS
• 3 code reviews (1 per iteration) + final comprehensive review — all PASS
• 3 simplification passes + final cross-file pass — all PASS
• Security regression checklist verified per iteration — 0 regressions

[Copilot]

Pull request overview

This PR addresses the full set of audit findings for the sigint plugin by tightening security controls, standardizing orchestration conventions (notably topic_slug), extracting shared protocols (config resolution + trend indicators), and expanding/strengthening eval coverage across skills, agents, commands, and documentation.

Changes:

• Standardize orchestration variables and tool permissions across skills/agents/commands; add resilience patterns (timeouts, blackboard/file dual-write, error handling).
• Improve prompt-injection and supply-chain security (input sanitization + <user_input> / <untrusted_data> boundaries; dependabot actor guard + SHA pinning; broaden SECURITY.md).
• Add shared protocols (CONFIG-RESOLUTION, TREND-INDICATORS) and extend eval coverage (new skill eval suites + regex-based deterministic checks).

Reviewed changes

Copilot reviewed 44 out of 45 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
skills/update/SKILL.md	Adds tool allowlist, input sanitization, <user_input> wrapping, topic_slug standardization, and timeout/partial-results guidance.
skills/trend-modeling/SKILL.md	Refactors trend indicator definitions to reference shared protocol; adds universal confidence tiers.
skills/trend-modeling/evals/evals.json	Converts checks to regex_match for trend-modeling eval assertions.
skills/trend-analysis/SKILL.md	Refactors trend logic section to shared protocol reference; adds universal confidence tiers.
skills/tech-assessment/SKILL.md	Adds shared trend indicator protocol reference + universal confidence tiers.
skills/start/SKILL.md	Adds tool allowlist, input sanitization, config resolution protocol usage, <user_input> wrapping, and error handling.
skills/start/evals/evals.json	Updates expectations from topic-slug to topic_slug naming and corresponding text.
skills/report/SKILL.md	Reorders/normalizes allowed-tools, adds sanitization, topic_slug propagation, date placeholder instruction, and <user_input> wrapping.
skills/report/evals/evals.json	Adds new unit-level evals for the report orchestration workflow.
skills/report-writing/SKILL.md	Fixes Mermaid line-chart guidance to use xychart-beta; adjusts full-report visualization conditions.
skills/report-writing/evals/evals.json	Converts legacy array eval format to {skill_name, evals} and updates deterministic check schema.
skills/regulatory-review/SKILL.md	Standardizes skill name slug, adds trend indicator protocol ref, updates disclaimer wording, adds universal confidence tiers.
skills/migrate/SKILL.md	Introduces new migration skill for legacy → v2 config with dry-run, backups, and topic discovery/context scaffolding.
skills/migrate/evals/evals.json	Adds unit-level evals for migrate (happy path, nothing-to-migrate, dry-run).
skills/market-sizing/SKILL.md	Standardizes skill name slug, adds trend indicator protocol ref, removes placeholder example value, adds universal confidence tiers.
skills/market-sizing/evals/evals.json	Converts legacy output_matches checks to regex_match.
skills/issues/SKILL.md	Expands/normalizes allowed-tools, adds sanitization, uses config resolution protocol for repo selection, fixes team name template, wraps user inputs.
skills/issues/evals/evals.json	Adds comprehensive unit-level eval suite for issues skill (repo resolution, dry-run, labels, no session).
skills/financial-analysis/SKILL.md	Standardizes skill name slug, adds trend indicator protocol ref, removes placeholders in scenario table, adds universal confidence tiers.
skills/customer-research/SKILL.md	Standardizes skill name slug, adds trend indicator protocol ref, adds interview applicability note, adds mandatory output rules + validation checklist + confidence tiers.
skills/competitive-analysis/SKILL.md	Standardizes skill name slug, adds trend indicator protocol ref, adds universal confidence tiers.
skills/augment/SKILL.md	Normalizes allowed-tools ordering/completeness, adds sanitization, improves section labeling, wraps user inputs in <user_input>.
skills/augment/evals/evals.json	Adds new unit-level evals for augment (happy path, no session, ambiguity, explicit methodology).
SECURITY.md	Adds threat model + in-scope categories + GitHub Security Advisories link; updates supported versions.
protocols/TREND-INDICATORS.md	Adds canonical shared definitions for INC/DEC/CONST + notation + usage rules.
protocols/CONFIG-RESOLUTION.md	Defines canonical cascade-based config resolution + context file loading behavior.
hooks/hooks.json	Updates session-start hook text to reference new config files and migration path.
evals/orchestration/evals.json	Updates topic_slug naming + regex_match usage; adds mono-repo multi-topic isolation eval.
evals/integration/evals.json	Strengthens conflict-resolution checks; adds multiple integration evals around v2 config resolution behaviors.
evals/commands/evals.json	Updates init/config expectations to v2 config and adds migrate/init regression tests.
evals/agents/dimension-analyst/evals.json	Converts a remaining output_matches check to regex_match.
docs/reference/configuration.md	Rewrites configuration reference for v2 JSON schema, cascade rules, and storage layout.
commands/status.md	Adds missing blackboard tool permission and updates topic_slug placeholder in blackboard scope.
commands/resume.md	Adds AskUserQuestion permission and updates topic_slug placeholders in file paths.
commands/report.md	Adds Mermaid validation tool permission to support report diagram generation.
commands/init.md	Replaces legacy sigint.local.md guidance with Config Resolution Protocol and v2 config template + legacy detection.
audit-results.md	Adds full audit findings report used as the change driver for the refactor.
agents/source-chunker.md	Fixes tool list ordering/completeness; adds explicit chunk size cap and SendMessage-based return path.
agents/research-orchestrator.md	Fixes tool permissions, topic_slug standardization, blackboard null-guard + dual-write, codex subagent type, <untrusted_data> boundaries, polling guidance, and ID stability guidance.
agents/report-synthesizer.md	Adds missing tool permissions; replaces wildcard blackboard reads with explicit per-dimension reads; standardizes topic_slug placeholders in paths.
agents/issue-architect.md	Adds missing tool permissions and adds local JSON fallback when GitHub MCP/gh aren’t available; standardizes topic_slug paths.
agents/dimension-analyst.md	Fixes tool permissions; renumbers gating steps; standardizes topic_slug placeholders and dual-write guidance.
.gitignore	Switches to gitignore sigint.config.json and adds .env / *.env / *.bak patterns.
.github/workflows/dependabot-automerge.yml	Adds dependabot actor guard and pins reusable workflow to a specific SHA.
.github/repo-metadata.json	Adds “MANUAL ONLY” warning note for apply command to prevent accidental execution.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.