[blainemotsinger]

Summary

Issue #40 had two parts. Part 1 (only architecture.md/review.md indexed) was already fixed by GH-36 / PR #39, so this PR hardens OrgKnowledgeFiles to index only regular files and pins it with a test. Part 2 is implemented here: write_knowledge and update_knowledge now accept org roots and store knowledge as markdown sections.

Changes

• knowledge/org.go: AppendOrgSection, ReplaceOrgSection, OrgSectionBody, and atomic SaveText, with sentinel errors for existing, missing, and duplicate sections.
• tools/org.go: org write/update handlers, bare-filename validation, org-<file>::<heading> id parsing, and Source: line folding/preservation.
• write_knowledge on an org root gains an optional file argument: summary becomes the ## heading, detail the body, and source a trailing Source: line. A missing file lists the available files, a bare new *.md name creates it, a heading collision points at update_knowledge, and rule is rejected.
• update_knowledge on an org root takes org-<file>::<heading>; only detail applies, the heading is immutable, the old Source: line is preserved, and the file must already exist.
• category is now schema-optional and required only for project stores.
• OrgKnowledgeFiles skips directories, broken symlinks, and other non-regular files while following symlinks to regular files.
• README, registry descriptions, install skill, examples, and the repo's own store entries (sub-003, dec-006) updated.

Verification

• gofmt -l clean
• go vet ./... clean
• go build ./... clean
• go test ./... 9/9 packages
• go test ./... -race -count=1 9/9 packages
• make eval-mock all PASS
• go run . debug --project . -> findings: ok none, doc count 12, zero warnings

Closes #40