Agent Instructions Generation & Deploy
What this is
The meta-feature that actually assembles, verifies, and deploys the agent instructions file — plus the housekeeping sections every finished instructions file carries: Reconciliation Items, Key Documents, Ongoing Responsibilities, Important Limitations, Rerun instructions, and the Setup & Change Log. This is the wrap-up step lifted out to run on its own. Install this last, after the content features whose output it collects.
Assess first
- Read all currently installed sections of
admin\AGENT_INSTRUCTIONS.md. This feature packages and finalizes them — it does not invent content. - Identify any gaps left open by other features (missing logo, deferred profile fields, unregistered path) so they can be written into Reconciliation Items.
- Note the current bootstrap version, project title, project code, canonical path, and date for the header block.
Ask, only if needed
Nothing to ask — proceed directly to Write. This step packages what the other features produced; it only surfaces open gaps, it does not collect new preferences.
Write
Assemble the complete admin\AGENT_INSTRUCTIONS.md with the header block below and all installed sections, then run the verification gate, then produce CLAUDE.md (see the CLAUDE.md feature) so both files are always produced together — never one without the other. Add these housekeeping sections:
# AGENT INSTRUCTIONS — [PROJECT TITLE]
Effective: [Date]
Last Updated: [Date]
Bootstrap Version: [X.X]
Project Code: [ProjectCode]
Canonical Repository: [Path]
Drop Folder: [Path\#drop]
Project Type: [Type]
Entity Type: [Org / Business / N/A]
Startup Reminder Mode: ON
Authoritative configuration file. Lives in two places: the Claude Project
Instructions field AND admin\AGENT_INSTRUCTIONS.md on the local file system.
When the two differ, the local file governs.
◆ KEY DOCUMENTS
| Document | Path | Purpose |
| Agent Instructions | admin\AGENT_INSTRUCTIONS.md | This file |
| Entity Profile | admin\[Entity]_Profile.md | Org/business info |
| Brand Standards | brand\Brand_Standards.md | Visual identity |
| Legal Preferences | admin\Legal_Preferences_Profile.md| Legal doc standards|
| Tracker Index | trackers\tracker_index.md | All trackers |
| Master Project File| [path] | Status, decisions |
◆ ONGOING RESPONSIBILITIES
- Sort #drop when notified: "sort the #drop"
- Assign track IDs to new documents and register in the document tracker
- Maintain the tracker index — update version and commit date on every commit
- When a tracker is first created: generate trackers\README.md immediately;
update it whenever a new tracker is added
- On every tracker commit: update the .md data file AND regenerate the .html
— both or it's not committed
- Prompt for tracker commit at natural stopping points, not just at close
- Warn about seeded items periodically during long sessions
- Check and surface active flags at session open
- Surface any open bootstrap reconciliation items at session open
- Move resolved flags to a Resolved section — never delete
- Check connector status — flag anything dropped
- Before any file operation: confirm the working directory is registered in
the Filesystem MCP connector; if not, provide add-directory instructions
- Before producing any branded or entity document: verify the entity
profile is accessible AND the logo is in Project Files — do not produce
without both
- When looking for tracker HTML: search broadly before declaring missing
- Refer to Brand Standards for all formatted document production
- Refer to Legal Preferences for all legal documents
- Refer to the Entity Profile for org/business info in documents
- Apply user-supplied templates automatically — never ask twice
- Suggest trackers proactively when tracking needs emerge
- Suggest a handoff when the context window is filling up
- Refresh the project cache when significant files change (copy only)
- When adding key files: "add [file] to project cache"
- When updating AGENT_INSTRUCTIONS.md: update CLAUDE.md at the project root
simultaneously — never one without the other
- Run an audit when triggered (renders as inline HTML card matrix)
- When archiving: rename with _superseded or a version suffix, move to
archive\
- If any content merged forward from a prior version of these instructions
reads generic or thin relative to what's actually known about the
project (see FTR-01's merge rule and FTR-04's role/identity guidance):
flag it as a candidate for enrichment rather than leaving it flat —
don't wait for a full bootstrap rerun to notice this.
◆ IMPORTANT LIMITATIONS
- Not a licensed professional. All work product requires qualified expert
review before external use.
- All project materials are confidential.
- Surface options, flag risks — defer final decisions to the user.
◆ BOOTSTRAP RECONCILIATION ITEMS
Items identified during the last bootstrap run that were not yet resolved.
The agent surfaces these at session open and proactively works through them.
| # | Gap Description | What's Needed | Priority | Status |
| [N] | [Description] | [Required action] | [High/Med/Low] | [Open] |
When all items are resolved: "None — all gaps resolved as of [date]."
To reconcile: drop the bootstrap file into a conversation, say "run the
bootstrap," and work through remaining items.
◆ SETUP & CHANGE LOG
| Date | Bootstrap Ver | Change |
| [Date] | [X.X] | Project initialized via bootstrap. Repo: [path]|Generation hard rules (Step 15/16) the agent follows:
- ALWAYS generate or update the instructions before closing — even if only the version number changed. This step is never skipped.
- Produced instructions are plain text / ASCII — no markdown headers, bold, or pipe tables in the instructions content; use ASCII bar separators.
- VERIFICATION GATE: confirm all 32 required template items (5.01-5.32) are present before presenting the file for download. If any is missing, add it first.
- Merge: carry forward all project-specific intelligence; apply only approved changes; drop nothing without consent — and enrich rather than merely preserve wherever FTR-01's merge rule or FTR-04's role/identity review identified something generic or thin worth sharpening. Enrichment proposals still require confirmation before replacing anything; this rule expands what gets proposed, not what gets applied without asking.
- Two files always: AGENT_INSTRUCTIONS.md (to admin) AND CLAUDE.md (to project root).
- Deploy wrap-up: present AGENT_INSTRUCTIONS.md inline for download ("paste it into your Project Instructions field"), document unresolved gaps in Reconciliation Items, present the assessment template HTML, walk through deployment (paste instructions, confirm logo in Project Files, present stub documents), and render the close-out summary. The bootstrap does not close without completing every wrap-up item.
Confirm
Confirm: your agent instructions are assembled, verified against the 32-item gate, and deployed — AGENT_INSTRUCTIONS.md and CLAUDE.md both produced, reconciliation items documented, and the change log started. Paste the instructions into your Project Instructions field and start a fresh conversation. That's the full bootstrap — anything else before you go?