> ## Documentation Index > Fetch the complete documentation index at: https://docs.pnbr.io/llms.txt > Use this file to discover all available pages before exploring further. # An entity rests on a trashed File > Trashing a File leaves its entities in the Graph with citations that no one can open, and nothing marks them until you look. Troubleshooting · graph > **Use when** > > A File was trashed or purged and the Graph holds entities that cite it, or an entity shows sources that will not open. > **Looking for something else?** > > A File replaced by a new edition (problem [Entities still cite a replaced version](https://docs.pnbr.io/troubleshooting/entities-cite-replaced-version.md)). A citation that waits for an answer after an edit (card [Citations to confirm](https://docs.pnbr.io/concepts/citations-to-confirm.md)). ## Signs * `penumbra files list --trashed` shows a File, and `penumbra context explore --file-id --json` still lists entities whose `files` hold that File ID. * `penumbra context entity ` still prints a `from:` line for the File. The line does not say that the File is trashed. * On MCP, `read` of the entity ends with a line that says some citations are not shown because their File is not readable. The entity can also say that it has no sources recorded. * `penumbra context materialize` warns with `graph_evidence_unavailable` for a citation, and the entity appears in the packet without that source. * After a purge, `penumbra files restore ` is refused with `file_content_purged`. ## Why it happens A trash takes the File out of reads and out of search. A citation names a File, a version and a content digest, and a trash changes none of them. So the entity keeps its citations, and no one can open the text behind them. The Graph does not read the Files side when a File is trashed. It keeps the entity and its citations as they were. The entity can still be right. The person may have trashed the File to tidy the project, or in error, or because the File is wrong. Penumbra cannot tell which. ## What Penumbra does By itself: * Keeps a trashed File, with its versions, until Penumbra purges it. Restore brings it back. * Leaves the entities and relationships that cite the File as they are. * Keeps each citation as it was written, with its File, version and content digest. * Lists the entity under the File ID in `penumbra context explore --file-id`. * Reads a trashed File as not found, so the exact text behind its citations cannot be opened. * Counts such citations on an MCP entity read and does not list them. * Leaves such citations out of a packet and warns with `graph_evidence_unavailable`. * Opens the citations again after a restore, with no change to the entity. You must: * Find the entities that cite the File before you trash it, and after. * Tell the person which entities lose a readable source, and let the person decide. Not handled: * No flag or recheck on entities when their File is trashed or purged. * No notice that tells you a File with entities was trashed. * The context commands do not say that a cited File is trashed. * After a purge, the File cannot come back, and its citations cannot be opened again. ## Do 1. Confirm the state of the File. `penumbra files list --trashed` lists trashed Files, and `penumbra files list --all` also shows `(purged)` in the PATH column. Note the File ID. 2. List the entities that cite it: `penumbra context explore --file-id --limit 200 --json`. Read the `files` list of each entity. Add `--cursor ` for the next page. MCP: none for this list. Use the CLI. 3. Keep the entities whose citations all point to trashed or purged Files or to older versions. Recipe [find-stale-entities](https://docs.pnbr.io/guides/find-stale-entities.md) does this for many Files. 4. Tell the person what you found. Give each entity with its name, its type and the File it cites. Ask what to do with each. 5. If the person trashed the File by mistake, restore it: `penumbra files restore `. A restore does not wait for approval (card rule [file.8](https://docs.pnbr.io/concepts/file.md#rule-file-8)). If it is refused with `file_content_purged`, the File is gone for good. 6. If another File holds the same fact, cite that File for the entity. Check the entity out in a workspace and stage the change with a citation of the live passage (recipe [review-and-submit](https://docs.pnbr.io/guides/review-and-submit.md), card rule [citations-to-confirm.11](https://docs.pnbr.io/concepts/citations-to-confirm.md#rule-citations-to-confirm-11)). 7. If the fact is no longer true, and the person says so, delete the entity: `penumbra graph delete `. An API key or a connected agent waits for approval (card rule [entity.4](https://docs.pnbr.io/concepts/entity.md#rule-entity-4)). ## Don't * Don't delete an entity because its File is trashed. A restore brings the source back, and the entity may be right. * Don't restore a File that the person trashed on purpose. Ask first. * Don't read the `from:` line as proof that the source opens. It names the File even when the File is trashed. * Don't trash a File to remove its entities. Trash leaves the entities in the Graph. ## Check * `penumbra files list --trashed` no longer lists a File you restored. * Or each entity that cited the trashed File cites a live File now. * Or the person has decided to keep the entity as it is. * On MCP, `read` of a refreshed entity lists its sources and shows no line about citations that are not shown. ## Related Cards [file](https://docs.pnbr.io/concepts/file.md) (rules [file.8](https://docs.pnbr.io/concepts/file.md#rule-file-8) and [file.9](https://docs.pnbr.io/concepts/file.md#rule-file-9)), [passage](https://docs.pnbr.io/concepts/passage.md) and [context](https://docs.pnbr.io/concepts/context.md). Recipe [find-stale-entities](https://docs.pnbr.io/guides/find-stale-entities.md). Problems [entities-cite-replaced-version](https://docs.pnbr.io/troubleshooting/entities-cite-replaced-version.md) and [two-editions-two-files](https://docs.pnbr.io/troubleshooting/two-editions-two-files.md). ## Keep going [File](https://docs.pnbr.io/concepts/file.md) · [Passage and citation](https://docs.pnbr.io/concepts/passage.md) · [Entity](https://docs.pnbr.io/concepts/entity.md) · [Context](https://docs.pnbr.io/concepts/context.md) · [Find entities that rest on an old version or a trashed File](https://docs.pnbr.io/guides/find-stale-entities.md) · [Entities still cite a replaced version](https://docs.pnbr.io/troubleshooting/entities-cite-replaced-version.md) · [A new edition is a separate File](https://docs.pnbr.io/troubleshooting/two-editions-two-files.md) Penumbra Grammar 0.6.26 This documentation is built and hosted on [Mintlify](https://mintlify.com), a developer documentation platform.