vault-cli: update paths for 0 System area restructure (flat 00/01/05/09 layout)

vault-librarian-prompt.md

@@ -6,7 +6,7 @@ Your job: keep the vault coherent, accurate, up to date, and ontologically sound
 2. The vault (JDex/map) lives at `/vault`; blob territory at `/data`. Notes are the map,
    files are the territory, joined by ID number — NEVER copy notes into /data.
 3. The authoritative topology is the manifest note
-   `0 System area/00 System category/00.05 Vault topology (machine-readable)`.
+   `0 System area/05 AI Agent/05 AI Agent.md`.
 4. All structural operations go through the `vault` CLI (on $PATH via Nix; `which vault`).
    Clobber-safe, dry-run by default, --execute to act, operates on BOTH trees + manifest.
    EVERY --execute op auto-commits to /vault git per-op — you never run `git add`/`commit` yourself.
@@ -43,11 +43,11 @@ Anything ambiguous or structural where the right answer needs Ryan's judgment:
 
 HOW to flag (two places, both required):
 1. APPEND a dated section to the Inbox note (via Obsidian MCP, append mode)
-   `0 System area/00 System category/00.01 Inbox for The Vault/00.01 Inbox for The Vault.md`
+   `0 System area/01 System Inbox/01 System Inbox.md`
    Header: `## Librarian flags — YYYY-MM-DD`. Under it, one `### N. <short title>` per flag with
    the issue, your recommended resolution, and the exact `vault` command you'd run if approved.
    Then commit ONLY that one file (safe even if Ryan's tree is otherwise dirty):
-     cd /vault && git add "0 System area/00 System category/00.01 Inbox for The Vault/00.01 Inbox for The Vault.md" \
+     cd /vault && git add "0 System area/01 System Inbox/01 System Inbox.md" \
        && git commit -m "Librarian: flags for YYYY-MM-DD"
    (This single-file add is the ONLY git command you run by hand — everything else auto-commits.
    Never `git add -A`.)
@@ -60,7 +60,7 @@ Local commits are invisible to Ryan until pushed. As the LAST action, push the v
 (Auto-fix ops committed per-op and the Inbox flag commit all get pushed together. If the
 push fails, say so in your final message — do NOT claim changes landed.)
 
-NOTE: the `0 System area/09 Archive of pre-RJFI tree` subtree is a SANCTIONED garbage dump
+NOTE: the `0 System area/09 System Archive` subtree is a SANCTIONED garbage dump
 (Ryan's ruling). NEVER flag, fix, or scan inside it — its broken links, stray files, and
 odd structure are all intentional/allowed. The tooling already excludes it.
 

vault_lib.py

@@ -99,7 +99,7 @@ def walk_structure(root, include_meta=False):
     return {"systems": systems, "areas": areas, "cats": cats, "ids": ids}
 
 
-ARCHIVE_SUBPATH = os.path.join(SYSTEM_META, "09 Archive of pre-RJFI tree")
+ARCHIVE_SUBPATH = os.path.join(SYSTEM_META, "09 System Archive")
 
 
 def is_archived(relpath):
@@ -237,7 +237,7 @@ def topology_diff(vault_root=VAULT, data_root=DATA):
 
 
 # ---- topology manifest (the 00-area source-of-truth note) ----
-MANIFEST_REL = "0 System area/00 System category/00.05 Vault topology (machine-readable)/00.05 Vault topology (machine-readable).md"
+MANIFEST_REL = "0 System area/05 AI Agent/05 AI Agent.md"
 MANIFEST_BEGIN = "<!-- VAULT-TOPOLOGY-JSON:BEGIN -->"
 MANIFEST_END = "<!-- VAULT-TOPOLOGY-JSON:END -->"