Fix allowed-tools to use spec-compliant space-delimited strings (#139)

* Fix `allowed-tools` to use spec-compliant space-delimited strings

Per the agentskills.io specification, `allowed-tools` must be a single
string of space-delimited patterns, not a YAML list. Converted all 23
SKILL.md files from the `- Item` list format to the correct
`"Item1 Item2"` string format. Also updated the frontmatter examples in
CLAUDE.md and the workflow-skill-design skill template to match.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* Fix remaining allowed-tools format in firebase-apk-scanner and workflow-skill-design docs

- Convert firebase-apk-scanner from comma-separated to space-delimited
- Update anti-patterns.md and tool-assignment-guide.md examples from YAML lists to space-delimited strings
- Remove unnecessary quotes from SKILL.md template placeholder

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* Cover commands, new SKILL.md files, and fix template placeholder

Extends the previous spec-compliance fixes:

* Convert command frontmatter (commands/*.md) — per Claude Code
  docs, command files use the same frontmatter as skills, so the
  same space-delimited rule applies.
* Convert three SKILL.md files added since the original PR:
  mutation-testing, trailmark-structural, trailmark-summary.
* Fix the placeholder in the workflow-skill-design template.
  The previous "[minimum tools needed, space-delimited]" was YAML
  flow-sequence syntax, which parses as a list — the opposite of
  what the placeholder claims. Replaced with a concrete-looking
  space-delimited example plus a comment.

Zeroize-audit agent files still use `allowed-tools:` in YAML list
form. They are intentionally excluded: per the project's own docs
(workflow-skill-design references), agents declare tools with
`tools:` (not `allowed-tools:`). Fixing those requires changing
the field name as well as the format and is out of scope for this
PR.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* zeroize-audit agents: switch allowed-tools to tools

Subagents declare their tool allowlist via `tools:` (comma-separated),
not `allowed-tools:` — see Claude Code's subagent docs and this
repo's own designing-workflow-skills/SKILL.md:47:

> Skills use `allowed-tools:` in frontmatter. Agents use `tools:`
> in frontmatter.

Before this change, the zeroize-audit agents declared their tool list
under `allowed-tools:`, which Claude Code does not read for subagents.
The field was effectively a no-op; the spawned agents had no tool
restriction enforced.

Renames the field on all 11 agents to `tools:` and reformats the YAML
list as comma-separated to match the documented format and existing
agents elsewhere in the repo (e.g. function-analyzer.md,
spec-compliance-checker.md). Tool sets are unchanged.

Behavior change: tools now actually constrain what each spawned agent
can call. The lists are the ones the original author intended.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* skill-improver: convert command allowed-tools to space-delimited

The two command files in plugins/skill-improver/commands/ still used
the JSON flow-array format (`allowed-tools: ["..."]`), which the rest
of this PR converted everywhere else. Convert them to the spec-compliant
space-delimited string form for consistency.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Dan Guido <dan@trailofbits.com>

plugins/zeroize-audit/agents/0-preflight.md

@@ -2,12 +2,7 @@
 name: 0-preflight
 description: "Performs preflight validation, config merging, TU enumeration, and work directory setup for zeroize-audit. Produces merged-config.yaml, preflight.json, and orchestrator-state.json."
 model: inherit
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Write
-  - Bash
+tools: Read, Grep, Glob, Write, Bash
 ---
 
 # 0-preflight

plugins/zeroize-audit/agents/1-mcp-resolver.md

@@ -2,16 +2,7 @@
 name: 1-mcp-resolver
 description: "Resolves symbol definitions, types, and cross-file references using Serena MCP for zeroize-audit. Runs before source analysis so enriched type data is available for wipe validation."
 model: inherit
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Write
-  - Bash
-  - mcp__serena__activate_project
-  - mcp__serena__find_symbol
-  - mcp__serena__find_referencing_symbols
-  - mcp__serena__get_symbols_overview
+tools: Read, Grep, Glob, Write, Bash, mcp__serena__activate_project, mcp__serena__find_symbol, mcp__serena__find_referencing_symbols, mcp__serena__get_symbols_overview
 ---
 
 # 1-mcp-resolver

plugins/zeroize-audit/agents/2-source-analyzer.md

@@ -2,12 +2,7 @@
 name: 2-source-analyzer
 description: "Identifies sensitive objects, detects wipe calls, validates correctness, and performs data-flow/heap analysis for zeroize-audit. Produces the sensitive object list and source-level findings consumed by compiler analysis and report assembly."
 model: inherit
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Write
-  - Bash
+tools: Read, Grep, Glob, Write, Bash
 ---
 
 # 2-source-analyzer

plugins/zeroize-audit/agents/2b-rust-source-analyzer.md

@@ -2,12 +2,7 @@
 name: 2b-rust-source-analyzer
 description: "Performs source-level zeroization analysis for Rust crates in zeroize-audit. Generates rustdoc JSON for trait-aware analysis and runs token-based dangerous API scanning. Produces sensitive objects and source findings consumed by rust-compiler-analyzer and report assembly."
 model: inherit
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Write
-  - Bash
+tools: Read, Grep, Glob, Write, Bash
 ---
 
 # 2b-rust-source-analyzer

plugins/zeroize-audit/agents/3-tu-compiler-analyzer.md

@@ -2,12 +2,7 @@
 name: 3-tu-compiler-analyzer
 description: "Performs per-TU compiler-level analysis (IR diff, assembly, semantic IR, CFG) for zeroize-audit. One instance runs per translation unit, enabling parallel execution across TUs."
 model: inherit
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Write
-  - Bash
+tools: Read, Grep, Glob, Write, Bash
 ---
 
 # 3-tu-compiler-analyzer

plugins/zeroize-audit/agents/3b-rust-compiler-analyzer.md

@@ -2,12 +2,7 @@
 name: 3b-rust-compiler-analyzer
 description: "Performs crate-level MIR and LLVM IR analysis for Rust in zeroize-audit. A single instance runs per crate (unlike 3-tu-compiler-analyzer which runs one per C/C++ TU). Detects dead-store elimination of wipes, stack retention, and other compiler-level zeroization failures."
 model: inherit
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Write
-  - Bash
+tools: Read, Grep, Glob, Write, Bash
 ---
 
 # 3b-rust-compiler-analyzer

plugins/zeroize-audit/agents/4-report-assembler.md

@@ -2,12 +2,7 @@
 name: 4-report-assembler
 description: "Collects all findings from source and compiler analysis, applies supersessions and confidence gates, normalizes IDs, and produces a comprehensive markdown report with structured JSON for downstream tools. Supports dual-mode invocation: interim (findings.json only) and final (merge PoC results, produce final-report.md)."
 model: inherit
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Write
-  - Bash
+tools: Read, Grep, Glob, Write, Bash
 ---
 
 # 4-report-assembler

plugins/zeroize-audit/agents/5-poc-generator.md

@@ -2,12 +2,7 @@
 name: 5-poc-generator
 description: "Crafts bespoke proof-of-concept programs demonstrating that zeroize-audit findings are exploitable. Reads source code and finding details to generate tailored PoCs — each PoC is individually written, not templated. Each PoC exits 0 if the secret persists or 1 if wiped. Mandatory for every finding."
 model: inherit
-allowed-tools:
-  - Read
-  - Write
-  - Bash
-  - Grep
-  - Glob
+tools: Read, Write, Bash, Grep, Glob
 ---
 
 # 5-poc-generator

plugins/zeroize-audit/agents/5b-poc-validator.md

@@ -2,11 +2,7 @@
 name: 5b-poc-validator
 description: "Compiles and runs all PoCs for zeroize-audit findings. Produces poc_validation_results.json consumed by the verification agent and the orchestrator."
 model: inherit
-allowed-tools:
-  - Read
-  - Write
-  - Bash
-  - Grep
+tools: Read, Write, Bash, Grep
 ---
 
 # 5b-poc-validator

plugins/zeroize-audit/agents/5c-poc-verifier.md

@@ -2,11 +2,7 @@
 name: 5c-poc-verifier
 description: "Verifies that each zeroize-audit PoC actually proves the vulnerability it claims to demonstrate. Reads PoC source code, finding details, and original source to check alignment between the PoC and the finding. Produces poc_verification.json consumed by the orchestrator."
 model: inherit
-allowed-tools:
-  - Read
-  - Write
-  - Grep
-  - Glob
+tools: Read, Write, Grep, Glob
 ---
 
 # 5c-poc-verifier

plugins/zeroize-audit/agents/6-test-generator.md

@@ -2,12 +2,7 @@
 name: 6-test-generator
 description: "Generates runtime validation test harnesses (C tests, MSAN, Valgrind targets) for confirmed zeroize-audit findings. Produces a Makefile for automated test execution."
 model: inherit
-allowed-tools:
-  - Read
-  - Write
-  - Bash
-  - Grep
-  - Glob
+tools: Read, Write, Bash, Grep, Glob
 ---
 
 # 6-test-generator

plugins/zeroize-audit/skills/zeroize-audit/SKILL.md

@@ -1,18 +1,7 @@
 ---
 name: zeroize-audit
 description: "Detects missing zeroization of sensitive data in source code and identifies zeroization removed by compiler optimizations, with assembly-level analysis, and control-flow verification. Use for auditing C/C++/Rust code handling secrets, keys, passwords, or other sensitive data."
-allowed-tools:
-  - Read
-  - Grep
-  - Glob
-  - Bash
-  - Write
-  - Task
-  - AskUserQuestion
-  - mcp__serena__activate_project
-  - mcp__serena__find_symbol
-  - mcp__serena__find_referencing_symbols
-  - mcp__serena__get_symbols_overview
+allowed-tools: Read Grep Glob Bash Write Task AskUserQuestion mcp__serena__activate_project mcp__serena__find_symbol mcp__serena__find_referencing_symbols mcp__serena__get_symbols_overview
 ---
 
 # zeroize-audit — Claude Skill