Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@docs/configuration.md`:
- Around line 74-82: The fenced code block under "Example Configuration" lacks a
language tag (triggering MD040); update the triple-backtick fence for the
environment variables example to include an "env" language specifier (i.e.,
change ``` to ```env) so the block containing ANTHROPIC_API_KEY, HTTP_PROXY,
HTTPS_PROXY, DEBUG, and MY_TOOL_PATH is fenced as env.

In `@docs/env-vars.md`:
- Around line 382-408: The markdown tables in docs/env-vars.md are not separated
by blank lines which triggers MD058; update the file so each table block (for
example the "Core Implementation", "Settings & Storage", and "Testing" tables)
is preceded and followed by a blank line, ensuring there is an empty line before
the opening | header row and after the closing row for each table so the linter
passes; no code changes required beyond inserting those blank lines around the
table blocks.
- Around line 45-110: The markdown has fenced code blocks without language tags
(the ASCII diagram under the top diagram block and the numbered steps under
"Data Flow: Settings → Spawned Process" / "For Terminal Sessions"); update those
fences to include a language identifier (e.g., change ``` to ```text) for the
diagram block and the numbered-list block so they pass MD040 linting while
preserving content and spacing.

In `@src/renderer/components/SettingsModal.tsx`:
- Around line 119-132: commitChanges currently writes entries into newEnvVars
even when validateEntry returns an error; update commitChanges (and use
validateEntry and EnvVarEntry) so that you only add an entry to newEnvVars when
validateEntry(entry) returns falsy (no error) and entry.key.trim() is non-empty.
Keep collecting errors into errors[entry.id] as before, call
setValidationErrors(errors), and only call setEnvVars(newEnvVars) after
filtering out invalid entries.
- Around line 1477-1505: The tooltip trigger (the wrapper div with className
"group relative ..." containing HelpCircle) is only hover-activated and not
keyboard-accessible; make it focusable by adding tabIndex={0} (or tabIndex={-1}
if you prefer programmatic focus) and ensure keyboard focus displays the tooltip
by relying on the existing "group-hover:block" behavior—replace or augment with
a focus-visible/focus:block approach (e.g., use group-focus:block or add a
focused class) so the sibling tooltip div becomes visible on focus as well; also
add outline-none to the trigger if following the style guideline and ensure the
tooltip content remains reachable/readable for screen readers.

---

Outside diff comments:
In `@src/main/ipc/handlers/process.ts`:
- Around line 403-445: The SSH handler is only passing effectiveCustomEnvVars to
buildSshCommandWithStdin so globalShellEnvVars never reach remote sessions;
update the code that constructs the env for buildSshCommandWithStdin to merge
globalShellEnvVars with effectiveCustomEnvVars (with session-specific vars
taking precedence) and pass that merged object as the env argument; reuse the
existing env-merge/tilde-expansion helper used elsewhere (or implement the same
merge logic) so tilde-expansion/stripping behavior matches local spawns and then
pass the mergedEnv into buildSshCommandWithStdin instead of
effectiveCustomEnvVars.

In `@src/main/process-manager/spawners/PtySpawner.ts`:
- Around line 69-90: The non-terminal PTY branch in PtySpawner currently sets
ptyEnv = process.env and therefore ignores shellEnvVars; modify the non-terminal
branch to merge shellEnvVars into the PTY environment (using the same
tilde-expansion/stripping rules as buildChildProcessEnv if needed) so that
agents running in PTY mode receive global env vars; reference the PtySpawner
code path that assigns ptyEnv, the shellEnvVars variable, and reuse
buildPtyTerminalEnv or buildChildProcessEnv to perform a safe merge rather than
a shallow overwrite.

---

Nitpick comments:
In `@src/__tests__/integration/process-global-env-vars.test.ts`:
- Around line 1-434: The tests are currently only asserting static objects and
don't exercise real behavior; either convert them to explicit todos or make them
true integration tests by wiring mocks/spies around the IPC handler and process
spawn flow: replace these spec-style describes/its with describe.todo/it.todo
and move the prose to docs if you don't want runnable checks, or implement mocks
that return configured global shell env vars from settingsManager and assert the
actual calls and data flow through the IPC handler → ProcessManager.spawn →
buildChildProcessEnv / buildPtyTerminalEnv (and any ChildProcessSpawner usage),
using spies to verify spawn was called with shellEnvVars and that environments
are merged correctly (also include tests for invalid/global/session precedence
by asserting merge behavior rather than static objects).

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/main/process-manager/spawners/PtySpawner.ts`:
- Around line 88-90: The PTY spawner currently only merges shellEnvVars into
ptyEnv and omits session-level customEnvVars; extract customEnvVars (and
isResuming if available) from the config in PtySpawner.ts and include them when
building ptyEnv—either call the existing buildChildProcessEnv(customEnvVars,
isResuming, shellEnvVars) like ChildProcessSpawner does, or merge with correct
precedence (ptyEnv = { ...process.env, ...shellEnvVars, ...customEnvVars }) so
customEnvVars override shell/global vars.