Instruction Layer Audit

01Result

Four sources carried standing instructions. Three were deleted; one remains.

Removed

17,432

bytes, across 8 files

Retained

2,136

bytes, global CLAUDE.md

Reduction

89.1%

of instruction bytes

Layers

4 → 1

file-based sources

Standing-instruction bytes by source

Measured with wc -c immediately before deletion.

Removed Retained

Account memory
6 files

9,475

LIMS/CLAUDE.md

4,464

IPO/CLAUDE.md

3,493

Global CLAUDE.md

2,136

09,475 bytes

Table view — removal ledger
Source	Path	Files	Bytes	Status
Account memory	`~/.claude/memory/*.md`	6	9,475	deleted
LIMS project	`Claudehome/LIMS/CLAUDE.md`	1	4,464	deleted
IPO project	`Claudehome/IPO/CLAUDE.md`	1	3,493	deleted
Global preferences	`~/.claude/CLAUDE.md`	1	2,136	retained

02Conflicts found before removal

The pre-removal audit compared the harness safety rules, both CLAUDE.md files, the six memory files, and the Model Context Protocol (MCP) server instructions.

Conflict	Sources	How it resolved
Visualize MCP banned in prose, still loaded as a tool	`IPO/CLAUDE.md:5` vs. the server's own tool description	The file won — the tool was never called. But the ban was prose, not enforcement.
“Never ask whether to publish” vs. the harness rule requiring permission to publish public content	Global `CLAUDE.md:35` vs. harness safety block	The standing rule counts as durable authorisation for `*.falconshire.com`. It does not extend to email, purchases, or form submissions.
Deliver the file vs. never hand over a file	`IPO/CLAUDE.md:14` vs. global `CLAUDE.md:37`	Reconcilable — send the file and lead with the URL — but the wording read as a prohibition.
“Keep replies concise” vs. mandatory footer, tables, expanded acronyms, verified/inferred split	`IPO/CLAUDE.md:67` vs. global `CLAUDE.md:18–24`	Format rules won; replies could not structurally be short.

One further defect was verified rather than inferred: the requirement that a publish slug start with claude appeared in IPO/CLAUDE.md:29 and in the memory store, but not in the global file — so a publish attempted from any other folder would have been rejected at preflight. The global file also gives the publish path as a literal ellipsis, …/Claudehome/sites/publish.py, which is not runnable.

03What stopped applying

Tone, format, autonomy, rigour and the publish-and-verify loop were verbatim duplicates of the global file and survive. These eight rules were not in the global file and are now gone in every folder.

Rule	Was at	Consequence
Visualize MCP ban	`IPO:5`	The `mcp__visualize__*` tools remain loaded, and their own description instructs that they be used.
Slug must start with `claude`	`IPO:29`	`publish.py` rejects any other slug at preflight.
Full `publish.py` path	`IPO:22`	Global has an ellipsis in place of the path.
`.aws-static-site.json` + `out/index.html` required	`IPO:28`	Preflight fails without both.
No bare `ssh`; route through `sitectl.py`	`IPO:32`	Bare `ssh` is blocked by the permission classifier.
Output-medium routing — `.xlsx` / `.docx` / matplotlib PNG / Mermaid inside HTML	`IPO:50–56`	No rule for non-web deliverables.
Chrome first for Shanghai Stock Exchange, Shenzhen, cninfo, HKEX	`IPO:42–44`	Back to retrying WebFetch on sites it cannot reach.
`launch.json` + `preview_start` for local-only viewing	`IPO:36–40`	No documented non-publish path.

LIMS/CLAUDE.md was not a preferences file. Its 94 lines were engineering documentation: the stack map and seven named invariants — quality-control thresholds as versioned data, no progression on a failed gate, analytics.py never returning protected health information, the agent never producing a number, chart palette slot order as the colour-blindness mechanism, unbroken sample lineage, and coordinated universal time (UTC) serialisation. The global preferences file cannot substitute for any of it.

README.md, REQUIREMENTS.md, docs/SOP_MAPPING.md and docs/VALIDATION.md survive in that project.

04Backup and restore

Eight files, 18,492 bytes, written before any deletion.

C:\Users\Administrator\.claude\backups\md-purge-2026-08-02-0525\
  CLAUDE.global.md                            2,136
  IPO\CLAUDE.md                               3,493
  LIMS\CLAUDE.md                              4,464
  memory\MEMORY.md                              756
  memory\autonomy-no-questions-finish-task.md  1,336
  memory\publish-web-deliverables.md           3,765
  memory\response-format-requirements.md       1,475
  memory\response-tone-and-style.md            1,068
  memory\rigor-verify-dont-guess.md            1,075

One backup file is not byte-verified. During the backup step a cp -a truncated the source IPO/CLAUDE.md to zero bytes at 05:25:35, before it was copied. That file was reconstructed in the backup from contents read at 05:23 in the same session — the 68 lines are correct, but unlike the others it could not be compared against the original, because the original no longer existed.

The other seven files were confirmed byte-identical with cmp before deletion.

05Open item

The memory directory is empty, but autoMemoryDirectory at ~/.claude/settings.json:3 still points at it, so new memory files can be written there in future sessions. Whether a setting exists to disable the feature outright is unverified — the claude.exe binary could not be located on this machine to check.