fix: honor changed_files from every config source and stop failing silently

CHANGELOG.md

@@ -8,6 +8,52 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
 
+### Fixed
+
+- `changed_files` is now honored no matter which way the config is built. It was
+  only resolved inside `create_config_from_args()`, so `INPUT_CHANGED_FILES` was
+  missing from the environment loader entirely (unlike `INPUT_SCAN_ALL` and
+  `INPUT_SCAN_FILES`) and any config built another way scanned the whole
+  repository. All sources now go through one resolver.
+- A raw `changed_files` string from a `--config` JSON file or a Socket dashboard
+  config is now resolved against git. `"auto"` used to be stored verbatim and
+  then iterated character by character, looking for files named `a`, `u`, `t`
+  and `o`, which scoped the scan to nothing.
+- `scan_all` still overrides `changed_files`, but now logs a warning naming the
+  scope it discarded. It can come from a Socket dashboard config rather than the
+  workflow, so discarding the request silently made diff-only mode look broken.
+  The warning also says that the override is partial: only the scanners that ask
+  `get_scan_targets()` for their paths widen, while the secret and container
+  scanners read `changed_files` directly and stay scoped, so setting both
+  produces a mixed run.
+- Pull request base resolution now falls back to `pull_request.base.sha` and
+  `pull_request.base.ref` from the GitHub event payload when `GITHUB_BASE_REF`
+  is unset, which is the case on any trigger other than `pull_request` and
+  `pull_request_target`. That covers `pull_request_review` and
+  `pull_request_review_comment`, whose payloads carry a top-level
+  `pull_request`. It cannot cover `issue_comment`, whose payload only has
+  `issue.pull_request` (URLs, no base ref or sha), so that trigger now gets a
+  warning naming itself and saying how to supply the base instead.
+- Changed-file detection now works inside the action's container. The scan runs
+  as root over a workspace owned by the runner user, which git refuses with
+  `detected dubious ownership`, so every diff failed and `changed_files: 'auto'`
+  or `'pr'` resolved to nothing. Nothing in a workflow could fix it: setting
+  `safe.directory` in a workflow step writes the runner's git config, not the
+  container's. When git refuses, the git reads now trust that one workspace
+  directory so the diff can run, and say so in the log. When git is not
+  refusing — any ordinary local run — nothing is relaxed.
+- A scope request that cannot be honored now says why. Shallow checkouts
+  (naming `fetch-depth: 0`), a workspace that is not a git repository, git
+  refusing to read the repository, and a missing PR base each log a specific
+  warning, and a scope that resolves to zero files warns that the scanners are
+  being skipped. All of these previously returned an empty list in complete
+  silence.
+- TruffleHog and Trivy no longer substitute their own staged-file scope when an
+  explicit `changed_files` request resolved to nothing. Trivy's filesystem
+  vulnerability scan also stops widening an empty scope back out to the whole
+  workspace; it is the one scanner that builds its own path list instead of
+  going through `get_scan_targets()`, so it needed the check twice.
+
 ## [2.2.1] - 2026-07-30
 
 ### Fixed

action.yml

@@ -112,12 +112,15 @@ inputs:
     description: >-
       Diff-only mode: scope every scanner (SAST/OpenGrep, secrets, containers)
       to changed files only, instead of the whole repository. Accepts a
-      comma-separated file list, a commit hash, 'auto' (diffs against the PR
-      base branch in CI, else staged changes), 'pr' (diff against
-      GITHUB_BASE_REF), or 'current-commit'. For PR/'auto' modes, check out with
-      actions/checkout fetch-depth: 0 so the base branch is available. When the
-      diff resolves to no existing files (e.g. a delete-only PR) the scanners
-      are skipped rather than scanning the whole repo.
+      comma-separated file list, a commit hash, 'auto' (the PR base diff when a
+      pull request base can be found, else staged changes), 'pr' (the PR base
+      diff only), or 'current-commit'. The PR base comes from GITHUB_BASE_REF or
+      from pull_request.base in the GitHub event payload. For PR/'auto' modes,
+      check out with actions/checkout fetch-depth: 0 so the base branch is
+      available. When the diff resolves to no existing files (e.g. a delete-only
+      PR) the scanners are skipped rather than scanning the whole repo, and when
+      the scope cannot be resolved at all the run logs a warning saying why.
+      Note that scan_all overrides this input.
     required: false
     default: ""
   scan_files:

docs/github-action.md

@@ -311,8 +311,9 @@ jobs:
 
 `changed_files` accepts:
 
-- `auto` — diff against the PR base branch in CI (`GITHUB_BASE_REF`), else staged changes
-- `pr` — diff against the PR base branch (`GITHUB_BASE_REF`)
+- `auto` — the PR base diff when a pull request base can be found, else staged changes
+- `pr` — the PR base diff, and nothing else
+- `current-commit` — files in the `HEAD` commit
 - a commit hash — files changed in that commit
 - a comma-separated file list — e.g. `src/app.py,src/utils.js`
 
@@ -322,6 +323,43 @@ jobs:
 > nothing rather than falling back to the whole repo. To scan an explicit file
 > list regardless of git state, use the `scan_files` input instead.
 
+### Checking that the scope took effect
+
+Diff-only mode logs what it did. Look for these lines in the step output:
+
+```text
+INFO  Resolved PR diff base to 'origin/main'
+INFO  Diff-only scan scoping requested (changed_files=auto): resolved 12 changed file(s)
+INFO  Diff-only scan scoping active: 12 scan target(s) from 12 changed file(s)
+```
+
+If the scope could not be applied, the run says why instead of quietly scanning
+everything or nothing:
+
+| Warning you will see | What to do |
+|----------------------|------------|
+| `none of the candidate PR bases (...) could be resolved ... The checkout is shallow` | Add `fetch-depth: 0` to `actions/checkout` |
+| `no pull request base was found` | The trigger is not `pull_request`, so there is no base. Use `changed_files: 'current-commit'` or an explicit file list |
+| `is not a git repository` | Run `actions/checkout` before the scan step |
+| `git refused to read ... not the usual container ownership mismatch` | The checkout is damaged or incomplete. Re-run `actions/checkout`, or pass an explicit file list |
+| `scan_all and a changed-files scope ... are both set, and they disagree` | Unset `scan_all` — it can come from a Socket dashboard config, not just your workflow |
+| `resolved to zero files. The scanners will be SKIPPED` | The diff found nothing scannable. Combined with a warning above, it tells you the diff failed rather than the PR being empty |
+
+You do not need `git config --global --add safe.directory` for this. The scan
+runs as root inside a container over a workspace owned by the runner user, and
+git normally refuses that with `detected dubious ownership`. When git refuses,
+the scan trusts that one workspace directory so the diff can run, and logs that
+it did — so no workflow change is needed. Setting `safe.directory` in a workflow
+step would not have helped anyway, because it writes the runner's git config
+rather than the container's. When git is not refusing, nothing is relaxed.
+
+### Where the setting can come from
+
+`changed_files` is honored identically from the action input, the
+`INPUT_CHANGED_FILES` environment variable, the `--changed-files` CLI flag, a
+`--config` JSON file, and a Socket dashboard config. `scan_all` outranks all of
+them; when it does, the run logs a warning naming the scope it discarded.
+
 ## PR Comment Customization
 
 Socket Basics automatically posts enhanced PR comments with **smart defaults that work out of the box** — clickable file links, collapsible sections, syntax highlighting, CVE links, CVSS scores, and auto-labels are all enabled by default.

docs/parameters.md

@@ -109,17 +109,74 @@ changed files only, the way Socket SCA Pull Request alerts behave. Accepts:
 
 - a comma-separated file list (e.g. `src/app.py,src/utils.js`)
 - a commit hash — files changed in that commit
-- `auto` — the PR base-ref diff when running in a PR CI context
-  (`GITHUB_BASE_REF` is set), otherwise staged (`--cached`) changes
-- `pr` — diff against the PR base branch (`GITHUB_BASE_REF`)
+- `auto` — the PR base diff when a pull request base can be found, otherwise
+  staged (`--cached`) changes
+- `pr` — the PR base diff, and nothing else
 - `current-commit` — files in the `HEAD` commit
 
+The same value works from the CLI (`--changed-files`), the `changed_files`
+action input, the `INPUT_CHANGED_FILES` environment variable, a `--config` JSON
+file, and a Socket dashboard config. Whichever way it arrives, it is resolved
+against git once, in the same place.
+
 Deletions are excluded from PR/`auto`/`pr` diffs so removed paths never become
 scan targets. When the diff resolves to no existing files (e.g. a delete-only
 PR), the scanners are skipped rather than falling back to scanning the whole
 repository. For PR/`auto`/`pr` modes, check out with full history (e.g.
 `actions/checkout` with `fetch-depth: 0`) so the base branch is available.
 
+**Finding the pull request base.** `auto` and `pr` try, in order:
+
+1. `GITHUB_BASE_REF` — set by GitHub on `pull_request` and
+   `pull_request_target` triggers only
+2. `pull_request.base.sha` from the event payload at `GITHUB_EVENT_PATH` — an
+   exact commit, so it works even when no remote-tracking branch exists
+3. `pull_request.base.ref` from the same payload
+
+Each candidate is tried as `origin/<ref>` and then bare. If none resolves, the
+run logs a warning naming what it tried and why (shallow checkout, workspace is
+not a git repository, git refused to read the repository, no PR base at all) and
+the scanners are skipped. **A scope request that cannot be honored is never
+turned into a whole-repository scan, and it is never silent.**
+
+Steps 2 and 3 cover the triggers whose payload carries a top-level
+`pull_request`: `pull_request`, `pull_request_target`, `pull_request_review`
+and `pull_request_review_comment`. They do **not** cover `issue_comment`. That
+payload has `issue.pull_request` instead, which is a set of URLs with no base
+ref or sha in it, so there is nothing to diff against without a GitHub API
+call. If you run the scan from a comment trigger, look the base up in the
+workflow and pass it in yourself:
+
+```yaml
+- id: prbase
+  run: echo "ref=$(gh pr view ${{ github.event.issue.number }} --json baseRefName -q .baseRefName)" >> "$GITHUB_OUTPUT"
+  env:
+    GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+- uses: SocketDev/socket-basics@v2
+  env:
+    GITHUB_BASE_REF: ${{ steps.prbase.outputs.ref }}
+  with:
+    changed_files: 'auto'
+```
+
+Otherwise the run warns that it was triggered by a comment on a pull request
+and that it cannot work the base out on its own.
+
+**Socket Tier 1 reachability is not diff-scoped.** It runs `socket scan reach`
+over the whole workspace because reachability needs the full dependency graph,
+so a `changed_files` scope does not narrow it. That is unchanged behavior, and
+the scanners this setting does scope are SAST/OpenGrep, secrets and containers.
+
+**`scan_all` outranks `changed_files` — but only for some scanners.** If
+`scan_all` is set — from `INPUT_SCAN_ALL`, a JSON config, or a Socket dashboard
+config — SAST scans the whole workspace and the changed-files scope is
+discarded. The secret and container scanners read `changed_files` off the config
+themselves rather than asking for scan targets, so they stay scoped to the
+changed files, and a run with both settings is a mix of the two. The run logs a
+warning saying exactly that, because `scan_all` often comes from a different
+place than the workflow that asked for diff-only scoping. Set one or the other,
+not both.
+
 **Example:**
 ```bash
 socket-basics --changed-files auto