fix: replace tilde paths with $HOME in v3.0 markdown instructions

[m4nt0de4]

Summary

Claude Code's Write/Edit tools use fs.writeFile() internally — they do not shell-expand ~. When the AI follows markdown instructions containing ~/.claude/... paths and passes them to Write/Edit tools, a literal directory named ~ is created in the current working directory instead of writing to the user's home directory.

This PR fixes 11 files across v3.0 where Write-facing markdown instructions used ~/.claude/ shorthand, replacing them with $HOME/.claude/ (with resolution notes where appropriate).

Root cause: The PAI system has two path systems:

• TypeScript tools (paths.ts, hooks) — use homedir() + join() → correct, unaffected
• Markdown instructions — use ~/.claude/ shorthand that the AI passes verbatim to Write/Edit → broken on all platforms

This is platform-agnostic — affects Linux, macOS, and WSL equally since Write/Edit are API-level file operations, not shell commands.

Files Changed (11 files, 20 insertions, 18 deletions)

File	Lines	Change
PAI/Components/Algorithm/v1.6.0.md	287, 664	PRD creation path + PATH RULE warning
PAI/SKILL.md	326, 703	Same (built version of Algorithm)
WorldThreatModelHarness/Workflows/UpdateModels.md	82, 86	Save/write model paths
WorldThreatModelHarness/SKILL.md	42	Model storage reference
Evals/Workflows/CreateUseCase.md	42, 100, 124, 176	4× Create file instructions
Evals/Workflows/CreateJudge.md	36	Create judge config
Evals/Workflows/CompareModels.md	49	Create comparison config
Evals/Workflows/ComparePrompts.md	79	Create comparison config
Research/Workflows/ExtractAlpha.md	382, 385	Scratch workspace + history paths
Agents/AgentProfileSystem.md	184	Agent profile creation
PAI/THEHOOKSYSTEM.md	163	Ratings write path

What Was NOT Changed

• Shell commands (mkdir -p ~/.claude/... in bash blocks) — shell correctly expands ~
• Read-only references (Read ~/.claude/...) — Read tool handles ~ correctly
• TypeScript code — already uses homedir() + join() via paths.ts
• User-facing documentation — ~ is fine in human-readable contexts

Testing

# Verify no Write-facing tilde paths remain in v3.0 skills:
cd Releases/v3.0/.claude/skills
grep -rn '~/.claude/' --include='*.md' | grep -iE '(create|write|save|work in)' | grep -v '```bash' | grep -v 'mkdir'
# Should return 0 results

Related

• Relates to plansDirectory: tilde (~) in path not resolved, creates literal ~/ directories #699 (tilde path expansion in plansDirectory setting)
• plansDirectory: tilde (~) in path not resolved, creates literal ~/ directories #699 addresses the installer/settings.json side; this PR addresses the AI-facing markdown instruction side

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