pixee organization preferences

PREREQUISITES: Read ../pixee-shared/SKILL.md for global flags, exit codes, and error handling, and ../pixee-auth/SKILL.md if authentication needs to be configured.

Organization preferences are a freeform markdown blob (≤10,000 characters) that the Pixee platform applies to every analysis run for the organization. The content shapes both triage (is a given finding a real risk for this org?) and remediation (how should the fix look in this codebase?), and is stored as a single document with audit metadata: content, updated_at, updated_by, org_id. The MVP hardcodes org_id to default-organization; an --org-id flag is planned once the platform supports multi-org.

pixee organization preferences get

pixee organization preferences get [--content-only]

• Default text output: a two-line Org: <id> / Updated: <iso> by <actor> header (colon separated, no tabs, because the markdown body is multiline and tabs are reserved for list commands), a blank line, then the content body emitted verbatim with no synthetic trailing newline.
• --content-only prints the body alone, byte-for-byte. Designed for piping into a file, less, bat, or a diff tool. No header, no trailing newline added.
• --output json (or --json) emits the full record including the HAL _links envelope. See ../pixee-api/SKILL.md for HAL conventions; do not restate them in scripts.
• When no preferences have ever been set, the command exits 0 with no stdout and writes a single line to stderr: no organization preferences set. Branch on this for fresh-organization flows.

pixee organization preferences set

pixee organization preferences set (--from-file <path> | --content <string>)

• Exactly one of --from-file or --content is required; passing both, or neither, is a parse error (exit 1) before any network call.
• --from-file - reads content from stdin, enabling get-transform-set pipelines.
• Content over 10,000 characters is rejected client-side before the round-trip with the observed character count in the error.
• Optimistic concurrency is handled internally: the CLI performs a GET, then PUTs with If-Match: <etag> (or If-None-Match: * on first creation). Agents and scripts never touch ETag headers directly.
• On HTTP 412, the CLI exits 1 with a friendly stderr line: concurrent modification: another writer updated organization preferences between read and write; re-run to refresh. Re-running typically succeeds; if multiple writers race repeatedly, refresh and re-author against the latest content.
• On success, output mirrors get (default header + body in text mode, full record in JSON mode).

Precedence and scope

Pixee resolves preferences per-analysis with strict fallback, no merging:

1. If the repository has PIXEE.md at its root (even if empty), it is used exclusively.
2. Else if organization preferences exist with non-empty content, they are used.
3. Else the analysis runs without preference guidance.

An empty PIXEE.md is a deliberate opt-out: a repo with one is treated as having preferences, which silently shadows org preferences for that repo. Agents working in a specific repo should check for PIXEE.md before assuming org preferences will apply.

Humans can author preferences in the Pixee web app under an organization's Settings → Preferences; the CLI and the web UI write the same resource.

Writing effective preferences

Preferences come in three flavors:

• Remediation guidance. How the team prefers to fix specific vulnerability classes: preferred libraries, internal utility classes, code patterns to use or avoid.
• Triage context. Why a finding may not be a real risk here: deployment architecture, compensating controls (WAF, network isolation, MFA), intentional patterns, false-positive zones.
• Rule preferences. Enable or disable specific scanner rules by tool name and rule ID, including marking rules as remediable when Pixee should attempt an automatic fix.

For worked examples of each flavor, see references/preferences-authoring.md. Treat those examples as starting points and adapt them to the org's stack, tone, and compliance posture.

Examples

# Print the body verbatim, suitable for piping into an editor or less
pixee organization preferences get --content-only

# Pretty-print the record as JSON, then pull a single field with jq
pixee organization preferences get --json | jq -r '.updated_by'

# Walk to the canonical resource via HAL (do not hardcode the path)
href=$(pixee organization preferences get --json | jq -r '._links.self.href')
pixee api "$href"

# Author offline and push from a file
pixee organization preferences set --from-file ./pixee-preferences.md

# Compose inline from a heredoc for a quick one-off
pixee organization preferences set --content "$(cat <<'EOF'
# Risk Guidance

## SQL Injection
Prefer Spring NamedParameterJdbcTemplate with :namedParameters.
EOF
)"

# Round-trip through stdin (byte-identical when the transform is a no-op)
pixee organization preferences get --content-only \
  | sed 's/old-vendor/new-vendor/g' \
  | pixee organization preferences set --from-file -

# Retry the set on concurrent-modification conflicts
until pixee organization preferences set --from-file ./pixee-preferences.md; do
  echo "retrying"
  sleep 1
done

Best practices

• Author non-trivial preferences as a file (typically pixee-preferences.md in a repo root or an internal docs repo) and push with --from-file. Reserve --content for one-liners and shell heredocs.
• Use --content-only when piping into editors, diffs, or less. Use --output json for programmatic inspection and HAL traversal.
• When composing preferences with help from external context (Notion pages, internal wikis, MCP-connected knowledge bases), draft the candidate document, route it through a human owner if the agent does not have authority to set org-wide policy, then push via --from-file once approved.
• Treat HTTP 412 as expected when multiple agents or humans edit concurrently. The friendly retry message is the contract; loop the set call or refresh and re-author against the latest content.
• Repo-level PIXEE.md silently overrides org preferences for that repo. Agents working inside a specific repository should check for PIXEE.md before assuming the org-level document applies.